The black-chinned tilapia Sarotherodon melanotheron heudelotii Rüppell 1852 (Teleostei, Cichlidae) is able to reproduce in a wide range of salinities (from 0 to nearly 120 psu). If the plasticity of the reproductive traits of S. melanotheron induced by salinity are now acknowledged, the underlying biological processes are still poorly understood, mainly because of the lack of genomic resources available for this species. The present study aimed at filling this gap, by generating a large transcript sequence collection, and identifying genes in male gonads subjected to changes in their expression according to salinity. The transcript collection was built from two major organs involved in reproduction, that is liver and gonads, collected from fish at all stages of sexual maturity and under different salinities. The purpose of this collection was to provide a first genomic resource in this species for which only a very limited number of sequences were available so far, and use it for identifying genes subjected to changes in their expression according to salinity.