Northern elephant seals (Mirounga angustirostris) exhibit some of the strongest anatomical and behavioral sexual dimorphism of any mammalian species. The degree of dimorphism at the microbial level, especially in young individuals, is still relatively unknown. Here, we investigated the interplay between sex, county of stranding, rehabilitation environment, and host genetics on the gut microbiomes of 44 northern elephant seal pups that were stranded along the California coastline and brought to a rehabilitation facility. Using a metabarcoding approach, we characterized microbial communities shortly after admission to the facility and found that both sex and county of stranding contributed to variation in microbial composition. Through population genetic analyses, we showed that the effect of county of stranding on microbial composition was not driven by underlying genetic structure. More broadly, we did not find any correlation between host genetics and microbiome dissimilarity, perhaps related to the extremely low genetic diversity of this bottlenecked species. Finally, we analyzed paired samples from a subset of 24 seals at two time points: shortly after admission to the rehabilitation facility and a month post-acclimation in the facility. Although microbiome compositions became more similar over time, sex continued to contribute to variation. Sex had a weaker effect on microbiome variation at the second time point in comparison to the first, potentially due to the homogenizing effects of rehabilitation. Our findings ultimately help shape our understanding of how environment and sex shape the gut microbiomes of young NES during an understudied period of development.