Background Revealing the specificity and flexibility of the algal symbiont-host association is fundamental for understanding how species can occupy a diverse range of habitats. Here we assessed the global distribution of the algal symbiont diversity for three shallow-water species of large benthic foraminifera (LBF) of the genus Amphistegina . Specifically, weinvestigated the role of habitat and host identity on the diversity of algal biome. Results Here we used next-generation sequencing to identify the algal biome in the species A. lobifera , A. lessonii , and A. radiata , collected from shallow habitats in 16 sites, spanning from the Mediterranean Sea to French Polynesia. Results showed the consistent presence of Fragilariales as the main algal taxa associated with all species across sites analysed. However, we uncovered unprecedented diversity of algal phylotypes found in low abundance.We further found high variability in algal biomes both within and between species and sites, indicating a substantial level of flexibility in symbiont associations. The effect of site was significant in all species analysed, and showed that local habitat is the main factor influencing the identity of algal symbionts. Symbiotic associations are also not constrained by the species identity nor the phylogenetic relationship among closely related hosts, suggesting symbiont identity plays a limited role in the evolutionary history of the genus Amphistegina . Conclusions We found that species of Amphistegina form flexible symbiotic relationship with algal taxa, which are primarily shaped by their local habitat. These observations strongly suggest that the capacity of Amphistegina species to utilise a diverse array of available symbionts likely underpins the ecological success of these crucial calcifying organisms across their extensive geographic range.