Urbanization and associated human activities are the main causes of biodiversity loss. Changes in land use, such as the transformation of forests into agricultural and livestock areas, the construction of roads and housing areas, and climate change, have led to the deterioration and destruction of a large number of habitats (CONABIO 2018; Vargas-Jaimes et al. 2021). In the present study, we computed the potential distribution and analyzed the structural connectivity of Ambystoma altamirani. These investigations improve the precision of the current information about the species and provide tools for various stakeholders to formulate comprehensive strategies. Such strategies can be executed effectively to change the course of species extinction. The principal challenge faced by amphibians, including Ambystoma altamirani, is the degradation of their habitat due to anthropogenic pressure. The Bosque de Agua region, where A. altamirani resides and is a microendemic species, serves as an example of this issue (Ávila-Akerberg et al. 2021; SEMARNAT 2018). According to our study on the potential distribution of Ambystoma altamirani, the species is found from north to south in the Bosque de Agua, with a greater presence in rivers and lakes within areas of Abies Forest surrounded by Pinus Forest. However, there is a low probability of presence in areas dominated exclusively by Pinus forest. This emphasizes the need for increased focus on the conservation of forests in the region, especially Pinus and Abies forests. Considering that the Bosque de Agua is part of the Trans-Mexican Volcanic Belt, considered one of the country's areas with the highest endemism (PROFEPA 2020), not only contributes substantial biological value but also complements significant hydrological value; these forests benefit more than 25 million people in the central part of the country who depend on the water supply retained by these ecosystems. Unfortunately, the loss of Abies and Pinus forests in the TMVB is increasing, with the highest recorded losses occurring between 2011 and 2014, principally in the southern part of the Bosque de Agua in areas such as Lagunas de Zempoala and Sierra de las Cruces-Ajusco-Chichinautzín (Vargas-Jaimes et al. 2021). These losses have occurred principally due to the occurrence of legal and illegal logging in the region, with a significant increase noted in activity even during the COVID-19 pandemic (López-García and Navarro-Cerrillo 2021), affecting all protected natural areas in the country (López-García and Navarro-Cerrillo 2021; González-Fernández et al. 2022). Highlighting the significance of the Trans-Mexican Volcanic Belt, 91.1% of the Abies forests in Mexico are located there (Sunny et al. 2017) and occupy a relatively small area within the Bosque de Agua: 34.9% Pinus forest and 17.3% Abies forest. Given their concentration and diversity, these areas warrant heightened attention and priority in conservation efforts. Our study also revealed that areas with land-use changes due to urbanization and agriculture have a negative impact on the species distribution in the region, which is information that is not known. In the first case, urbanization stands out as one of the main causes of biodiversity loss and the generation of global warming. The overexploitation of resources, such as the aforementioned logging and certain practices and customs recommending Ambystoma as food, contributes to these negative effects. Additionally, the introduction of exotic species, such as rainbow trout (Oncorhynchus mykiss), into the habitat of A. altamirani heightens these challenges. The rainbow trout competes for food with A. altamirani, feeds on their eggs and larvae, acts as a vector for diseases caused by waste, and induces changes in the territory, feeding, and mating behavior of the species, leading to a reduction in the effective population size (Knapp and Matthews 2000; Zambrano et al. 2010; Pilliod et al. 2013; Martín-Torrijos et al. 2016). In the second case, the central region of the country is one of the main agricultural producers; soil with high water retention is a factor that results in the productive potential of the area; and corn, potatoes, and oats are some of the main crops. The impact on A. altamirani lies in the fact that the majority of farmers in Mexico still cultivate their land using traditional planting and harvesting methods, resulting in soil erosion and degradation while wearing down the species' habitat. Additionally, and certainly not less significant with a great negative impact, is the use of agrochemicals as the main stimulus for crop growth (Valbuena et al. 2021), which can result in severe socioenvironmental consequences. This includes the prediction that in the next 50 years, a minimum of 25% of the biodiversity we currently know may be lost (Lanz et al. 2018). The soil, air, and water (where A. altamirani resides) are contaminated with chemicals that increase vulnerability to disease. On the other hand, within the analysis of structural connectivity, we observed that the most important area for Ambystoma altamirani connectivity (core areas) is in the center of the Bosque de Agua. This may be because this region experiences the least land use changes, and the species can easily connect with other populations. According to our analysis, barriers and bottlenecks have not yet severely affected this region. Therefore, the central zone could be where the greatest diversity and genetic variation in A. altamirani populations exist. Additionally, to identify the corridors that presented higher or lower costs for the flow of A. altamirani populations, we included the 6,866 roads found in the study area. The genus Ambystoma is considered among the philopatric species based on its migratory distance capacity (Orloff 2011). Given this information, within the analysis of structural connectivity, we used a range of 500–1000 m as a reference for migratory distance. We found that when applying a stricter mobility restriction (500 m), the opportunity to find corridors with lower connectivity costs for Ambystoma altamirani is also lower than that for a 1000 m/1 km restriction, which tends to be more abundant (Orloff 2011). This is important because this information provides more detail about where the barriers preventing the flow of Ambystoma altamirani are located at a more detailed scale given the shorter distance. This approach can facilitate the inclusion of conservation strategies by precisely addressing crucial areas in the region, starting with those that lack any protection. Overall, as a first step, it is recommended and urgent to protect the central zone of the Bosque de Agua, where the flow between populations of A. altamirani is significant and where the habitat of the species is not currently observed to be severely fragmented. Without any kind of strategy for shielding the area, the area is highly vulnerable to land use changes that do not bring benefits. These changes will, in turn, increase barriers in the highly connected zone, leading to more bottlenecks and a greater risk of extinction for microendemic species. While it is important to protect the region from north to south given the distribution of A. altamirani, the first visible suggestion is the protection of the central zone of the Bosque de Agua through natural protected areas (ANPs). According to our analysis, there are no federal or state-designated Mexican protected areas for the region with the highest connectivity of A. altamirani in the Bosque de Agua. This approach is not the only alternative available; although Mexican Natural Protected Areas (ANPs), as in other parts of the world, have been part of environmental damage mitigation due to their advantages and opportunities (de Manantlán 2023), this does not mean that within these limitations, there is no exploitation of natural resources such as water pollution, soil contamination, urbanization, livestock farming, agriculture, or other anthropogenic activities that affect diversity. Additionally, other problems exist, such as disputes over territory; spaces that can be federal, state, communal, or private; where as mentioned by Hensler and Merçon (2020); habitants generally lose certain rights, including usage and management; and access and ownership, ending up as legal delimitations and definitions of a space with different interests of its owners (Arriola et al. 2014; Hensler and Merçon 2020), most of which are distant from biodiversity conservation. In this scenario, we include the dynamism with which land use changes are carried out in the Bosque de Agua. From a macroscopic perspective, relatively small areas can be found within the region where over two decades, there has been constant logging, deforestation, afforestation, and land use changes (López-García and Navarro-Cerrillo 2021). From this perspective, we can understand the gap in information and the limited amount of information available when we visualize the difficulty in accurately determining the potential distribution and connectivity of A. altamirani. However, this is not the reflection but rather the fact that some actions taken regarding changes within the region have become irreversible. For example, the construction of a road, which requires a certain number of trees to fall, brings about changes in an ecosystem that may not be deemed significant by the construction company. The authors may argue that the deforested forest area will be minimal and that any damage will be mitigated through a reforestation program. As a result, in most cases, the reforested trees do not survive due to their species and the characteristics of the new site. Therefore, new forests will never replace previous forests, and the habitats within these forests will also suffer significant fragmentation, reducing the survival success of these species (Martínez et al. 2020). In this sense, we suggest strategies and actions that consider the environment "systems thinking," where all the parts and actions interact and affect each other. Over time, we become more aware that the actions we take, whether positive or negative for the environment, will have a two-dimensional effect in which the impact will be reflected in the way we live. Therefore, returning to the previous example, it is understandable that after some time, floods may worsen in towns near the new road, as there is no longer enough forest to retain the water. This is not always considered in the affirmative response given by different stakeholders before any change or exploitation of resources. As the author Zambrano (2014) mentions, "a very small change in variables can generate gigantic changes in the response" (Zambrano 2014; Ceccon y Martínez-Garza 2016; Hensler and Merçon 2020; Martínez et al. 2020, Tengö et al. 2021). We do not mean to say that the management of strategies and their actions is simple; systems are complex, and above all, they are neither permanent nor eternal. However, to increase the probability of achieving the desired outcomes, it is suggested that such strategies be carried out based on shared governance (Cambronero et al. 2018; Fournier 2016; Valverde Garnica 2016), where the plurality of actors and different hierarchies, considering the local community of the region, their knowledge, participation, and consultation, focus on carrying out collective actions under the same interests: the conservation of biodiversity, its species, and the sustainable management of resources.