There is a reciprocal relationship between the gut microbiome and its host. The microbiome influences host health and survival, while host traits shape the microbial community structure. One of the ways the host is thought to influence the microbiome is through the major histocompatibility complex (MHC). The MHC is a collection of variable genes that play key roles in host immunity. However, few studies have examined wild animal populations for links between the MHC and microbiome. To close this gap, researchers examined the MHC genotypes and gut microbial communities of wild Seychelles warblers (Acrocephalus sechellensis). Specific MHC alleles, rather than overall MHC diversity, corresponded to differences in the diversity and composition of the microbiota and MHC class I alleles had a greater impact on the microbiota than MHC class II alleles. Gut microbiome diversity also increased with whole-genome heterozygosity, which is the proportion of sites in the genome with two different alleles. While further research is needed to determine if these connections are direct or indirect and if they impact host fitness, the results demonstrate that both the host immune system and host genotype can modulate the gut microbial community of wild animals.