All eukaryotes have associated communities of microbial organisms, termed the microbiome, which confer a variety of important physiological processes. When the host-microbial relationship is disrupted, often the host suffers change in physiological functioning, and in extreme instances can result in mortality of the host. Each host organism harbors a distinct microbiome. From globally distributed hosts, we expect pattens of biogeography to occur in the microbiome, but to the extent variability occurs remains unknown. Here, we analysed the microbiome from the epidermal surface of Rhincodon typus (whale sharks), across distinct oceanic regions of the world and described the microbial taxonomic and gene function compositions using shot-gun metagenomics. In addition, we used network analysis to investigate whether there was inherent structure in the microbiome regardless of underlying diversity patterns. Microbiome alpha and beta diversity patterns were distinct, across five sites which included Cancun, Mexico; Mafia Island, Tanzania; Ningaloo Reef, Australia; Oslob, Philippines; and La Paz, Mexico. The highest and lowest taxonomic alpha diversity occurred on sharks from Ningaloo (H` = 3.79 ± SD 0.47) and Cancun (2.99 ± 0.24), while alpha diversity at Ningaloo was distinctly low (H` = 4.31 ± 0.03). Taxonomic (F df = 4,70 = 4.77; R2 = 0.21; p < 0.01) and gene function (F df = 4,70 = 28.05; R2 = 0.61; p < 0.01) beta diversity were also distinct, with locating having a larger effect on gene function relative to taxonomic beta diversity. Despite effects of biogeography on diversity patterns, the microbiomes of the whale sharks have network structures indistinguishable from Erdos-Renyi type network structure for both taxonomic and gene function patterns, suggesting similar inherent structuring patterns among locations. Therefore, the microbiomes, while having distinct diversity patterns appear to have similar microbiome complexity. We suggest that despite having different microbiome composition, the underlying ecological dynamics influencing the epidermal microbiome remains the same across whale shark groups around the world.