Conflicting results have been reported concerning the ability of c-kit-positive bone marrow cells (c-kit-BMCs) to transdifferentiate into cardiomyocytes in vivo. We have raised the possibility that c-kit-BMCs may constitute a functionally heterogeneous pool, containing cells with different cardiomyogenic potential. To test this hypothesis, clonal analysis of individual c-kit-BMCs was introduced to track in vivo the progeny derived from a single founder cell. By employing viral gene-tagging, only a limited fraction of clonal c-kit-BMC was found to be able to generate cardiomyocytes in the acutely infarcted heart. On this basis, c-kit-BMC-derived clones were classified as myogenic or non-myogenic. The gene profile of these two categories of cells was studied by RNA-sequencing to determine whether myogenic c-kit-BMCs had a distinct molecular signature. Genes that showed a significant (p<0.05) expression difference of at least 2-fold among cell groups were included in the analysis; 1243 genes were upregulated and 493 genes were downregulated in myogenic c-kit-BMCs when compared with non-myogenic c-kit-BMCs. An additional comparison involved freshly isolated c-kit-BMCs. 2512 genes were upregulated in myogenic c-kit-BMCs and 1844 genes were downregulated in this cell group. These results were subjected to functional annotation using gene ontology for the identification of molecular pathways showing different state of activation or repression in myogenic BMCs. The affected transcripts in myogenic c-kit-BMCs involved mostly signal transduction and muscle development including cardiac muscle. Similarly, a set of genes implicated in the regulation of angiogenesis were more represented in myogenic c-kit-BMCs, possibly reflecting the proficiency of this cell class to form vessels in the microenvironment of the infarcted heart. Our findings document that myogenic clonal c-kit-BMCs have a distinct molecular signature that differs from that of non-moygenic and non-expanded c-kit-BMCs. On this basis, c-kit-BMCs with high cardiomyogenic ability can be prospectively isolated and employed clinically for the treatment of patients with cardiac diseases.