Comprehensive understanding of tissues and organs development requires a detailed description of tissues specific developmental programs. In particular, Gene Regulatory Networks need to be analyzed at the tissue level, requiring organ specific transcriptional landscapes to be established. Here, we describe an efficient and stringent strategy for cell purification of differentiating cells from Drosophila embryos by flow cytometry. This, combined to mRNA amplification, can be used for transcriptomic analysis of small, tissue-specific cell populations. We present an application to the Drosophila cardiac system, whose cell population represents 0.5 to 1% of total cells within the whole embryo. Based on widely available fluorescent reporter transgenes, this method should be applicable to a number of tissues and organs.