Macroalgae play important ecological roles, including as hosts for a wide range of epifauna. However, the diversity relationships between macroalgae and epifauna are poorly understood for most tropical host species and algal morphologies. This study aims to characterize and analyse the diversity of invertebrates present amongst macroalgae with three distinct morphologies (three-dimensional, filamentous and foliose) across different tropical intertidal sites in Singapore. Morphological and DNA barcoding tools were employed for epifaunal species identification, and ordination statistics and multiple linear regression were used to test the effects of algal morphology, species and site on community structure and diversity of epiphytic invertebrates. Overall, epifaunal communities were distinct among sites and algal morphologies, and diversity was affected significantly by algal morphology. In particular, filamentous macroalgae hosted the highest abundance of epifauna dominated mainly by amphipods, which were able to take advantage of the high surface area to volume ratio in filamentous algal mats as a consequence of their thinner forms. Foliose species showed a significantly negative effect on invertebrate diversity. Our findings highlight the diverse associations between intertidal macroalgae and invertebrates with high turnover between algal morphology and sites that contribute to the high biodiversity of tropical shores. Future studies should consider the effects of the host habitat, seasonality and more algal species on epifaunal diversity.