The transcriptome of the brackish water amphipod Gammarus chevreuxi was sequenced at three stages of development using 100 BP paired-end Illumina HiSeq sequencing. Stages relevant to the ontogeny of heart function were selected: no heart structure present, presence of non-functional heart (i.e. not beating) and presence of functional heart (i.e. regular heart beat). The generated data is a valued contribution for an ecologically-important aquatic invertebrate.