Fish catches around the Great Lake, Tonle Sap river and the transitional zone between the lake and the river were studied by professional ‘fishing lot' (i.e. fishing zone) from 1995 to 1997. One hundred and twenty species of fish, belonging to 26 families and nine different orders were recorded. Compared to previous studies (1936–1976), only 53 % of families, 32 % of genera and 54 % of species were collected by professional fishing lot. This important loss in biodiversity could have several causes: bias of sampling procedures between professional fishing and research sampling, overfishing, modification of the floodplain by deforestation, etc. The professional fishing data showed that Cypriniformes accounted for 41.6 % of the total number of individuals caught, the Cyprinidae family alone represented 40 species. Siluriformes made up 21.6 %, Perciformes 13.3 %, with six other orders represented by smaller numbers. Eighty-seven percent of the recorded species occur in both habitats depending on the season. Migration takes place from the Mekong river to the Great Lake through the Tonle Sap river at the beginning of the rainy season (May–October), and in the reverse direction at the start of the dry season (November–February). The majority of the species reproduce at the start of the rainy season (May–June) in the flooded plain and the forest floodplain of the Great Lake; the period, the place and the means of reproduction have not been closely studied, particularly for the Belontiformes, Clupeiformes, Synbranchiformes, Pleuronectiformes and Tetraodontiformes. Multivariate analysis of fishing data (November–February) shows three distinct communities: that of the lake (Perciformes and Siluriformes), of the river (Pleuronectiformes, Cypriniformes, Clupeiformes and Siluriformes), and of the transitional zone formed from the principal channel, the old river channel and the oxbow lakes (Cypriniformes, Siluriformes and Osteoglossiformes).