Abstract: Investigation on copepod communities in Perai river estuary was conducted from November 2005 to May 2006. Five stations were established for monthly sampling and were located from the river mouth to the upper reaches of the river. Copepod samples were collected from vertical tows using a standard zooplankton net. The Perai river estuary was slightly stratified and salinity decreases significantly from the mouth of the river towards the upper reaches of the river. A total of 28 species of copepods were recorded and comprised of 14 families, Paracalanidae, Oithonidae, Corycaeidae, Acartiidae, Calanidae, Centropagidae, Eucalanidae, Pontellidae, Pseudodiaptomidae, Tortanidae, Ectinosomatidae, Euterpinidae, Clausidiidae and Cyclopidae. A total of 10 species showed high positive affiliation towards salinity (R>0.60), Acartia spinicauda, Euterpina acutifrons, Microsetella norvegica, Oithona nana, Oithona simplex, Paracalanus crassirostris, Paracalanus elegans, Paracalanus parvus, Pseudodiaptomus sp. and Hemicyclops sp. The copepod species Pseudodiaptomus dauglishi were negatively affiliated towards salinity (R = -0.71). The copepod assemblages classified into two distinct groups according to salinity regimes, euryhaline-polyhaline group (25 marine affiliated species) and oligohaline-mesohaline group (3 freshwater affiliated species).