Whale shark epidermal microbiomes are species specific. Here we analyse whether the microbial taxa vary across sex and size of the host individual and whether the microbiome on the same individual varies across each day, measured for 3 -4 days. The analysis showed the relative abundance of microbes was not significantly different between host size categories (PERMANOVA p = 0.656) or sex (PERMANOVA p = 0.699). However, there is a significant difference in the shark skin microbiome across days (PERMANOVA p= 0.001). To investigate the difference in microbes, we used 26 metagenome assembled genomes (MAGs) to identify whether the varying microbes showed functional redundancy. Of the 26 MAGs used, 6 were found to be novel. We discovered how the microbes present influences gene function of the whale shark skin microbiome. Sphingomonadales and Alteromonadales appeared to be switching across days and suggest that as Alteromonadales decreases in abundance and gene count across days, Sphingomonadales increases to replace the functional role. We found that Alteromonadales and Sphingomonadales have similar key functional roles on the skin microbiome, particularly in motility and chemotaxis, respiration, and membrane transport efflux systems. Microbes may act as an early warning system, particularly for the aggregation at Oslob in the Philippines, which has high levels of human interactions associated with tourism. Our findings here provide insight for further studies to explore human interactions and how this influences the whale shark skin microbiome, gene function and potentially host health.