The rapid and extensive destruction of mangrove forests and adjacent peritidal ecosystems in the Indo-Pacific region requires the development of efficient management and conservation actions. Mudskippers (Gobiidae: Oxudercinae) are amphibious gobies that are strictly linked to mangrove forests and tropical mudflats. I recorded the presence and habitat distribution of mudskipper species in four mangrove ecosystems along the west coast of Peninsular Malaysia. Different localities host different mudskipper communities, while in each locality species are differentially distributed along the intertidal gradient. At the ecosystem level, I found a significant exponential correlation between sampled area and the species richness of these communities, consistent with the SAR hypothesis. At the habitat level, the presence of a vertical zonation along the intertidal gradient suggests the possibility of using the species living exclusively in higher or lower levels as bioindicators for habitat anthropogenic impact, respectively from the land and from the sea.