Intraspecific colour polymorphisms have been the focus of numerous studies, yet processes affecting melanism in the marine environment remain poorly understood. Arguably the most prominent example of melanism in marine species occurs in manta rays (Mobula birostris and M. alfredi). Here, we use photo identification catalogues to document the frequency variation of melanism across Indo-Pacific manta ray populations and test for evidence of selection by predation acting on colour morph variants. We use mark-recapture modeling to compare colour morph survivorship in three M. alfredi populations and assess the relationship between frequency variation and geographical distance. While large differences in melanism frequencies existed among populations of both species (0-40%), apparent survival estimates revealed no difference in survivorship between morphs. We found a significant association between phenotypic and geographical distance in M. birostris, but not in M. alfredi. Our results suggest melanism is not under selection by predation in the tested M. alfredi populations, and that frequency differences across populations of both species are a consequence of neutral genetic processes. As colour polymorphisms are often subjected to complex selection mechanisms, our findings only begin to elucidate the underlying evolutionary processes responsible for the maintenance and frequency variation of melanism in manta ray populations.