A comparative study of the fish communities in two lake ecosystems in Mali (Lakes Manantali and Selingue) was based on monitoring small-scale fishery landings for a 13-month period. The main difference between the two lakes is the fishing pressure, being higher in Lake Selingue and lower in Lake Manantali. The effects of fishing on the structure of the fish communities in the two lakes were analysed with the use of diversity indices, rank species abundance (RSA) and abundance-biomass comparative curve (ABC) methods. The diversity differed significantly between the lakes, being higher for Lake Selingue. Analysis of the community structure, using RSA curves, indicated a more regular distribution of the weights between fish species for Lake Selingue than for Lake Manantali. The two lakes exhibited different exploited fish community structures. For Lake Selingue, the fishery was based on smaller-sized species, compared to that for Lake Manantali. The indicators based on the species composition of exploited fish communities, in terms of abundance and life-history traits, seemed to be more relevant in this study. Indicators such as diversity indices and RSA curves depend strongly on the exploitation strategy, being unreliable for evaluating exploited fish communities from catch data.