Polymorphism may allow individuals to expand habitat use through morph-specific resource demands. However, the underlying mechanisms maintaining different morphotypes in nature are difficult to identify. We sampled populations of the shrimp Hippolyte obliquimanus in the macroalgae Sargassum furcatum and Galaxaura marginata to examine morph-specific distribution patterns, population structure and female reproductive output, as an initial step to understand polymorphism in this species. Two main colour morphotypes were identified: homogeneous shrimps (H), which change their colour, mostly from pink to greenish-brown tones, and striped translucent shrimps (ST), whose colour remain unaltered. Distribution of individuals between habitats was clearly morph-specific. H shrimps occupied colour-matching substrates, mainly Sargassum, where they can attain large densities, and ST individuals were evenly distributed in both algae. Brood production and size-fecundity relationships were similar between morphs and habitats, suggesting these are relatively fixed traits in the population. However, sex proportions, defined as the male to female ratio, were different between morphs and macroalgae. H shrimps were chiefly females (1:2.04) and ST shrimps mostly males (1:0.30). Given the likely polygynic pure-search mating system in H. obliquimanus, the female-biased sex ratio observed in Sargassum is apparently more advantageous than the Mendelian proportion found in Galaxaura habitat. Clustering on vegetated habitat, the female-biased H morph may be relatively cryptic and sedentary, compared with the male-biased ST morph which apparently combines a more neutral camouflage strategy to a generalized habitat use. Altogether, results suggest that selection for sex-specific traits favours the maintenance of polymorphism in H. obliquimanus.