Drosophila has been instrumental in identifying novel genes and pathways required for heart development, and in uncovering the genetic and molecular causes of heart disease. However, unlike other model systems (mouse, zebrafish and even sea urchin) and humans, single-cell RNA-seq data had been missing for the hugely valuable fly model. Here we provide data from over 3,000 Hand-GFP embryos, collected over five consecutive developmental stages (stages 13, 14 early, 14 late, 15, and 16) known to be critical for healthy heart development in the fly; ranging from bilateral rows of cardiac progenitors to a fused and beating heart tube. Hand is a well-established and widely used marker for Drosophila heart cells, and the only known marker to be expressed throughout development, from embryos to adults. Data included here are obtained by 10X Genomics sequencing of GFP positive (by FACS) cells, and further selection of the “heart” cell cluster (see SCP1469 for all GFP+ cells) based on the expression of known cardiac genes. The single cell transcription profiles for the “heart” revealed six subclusters, i.e. cardiac cell types (cardioblasts and six types of pericardial cells) in the developing Drosophila heart.