Blast appearing cells in the peripheral blood and bone marrow may occasionally arise from non-hematopoietic tissues. We present a 58 year old female who presented at our emergency room with symptomatic pancytopenia. Several months earlier she was diagnosed and treated for rhabdomyosracoma of the nasopharynx and entered remission. When we examined the bone-marrow aspirate we estimated the number of blasts at 25 %. Based on this evaluation, a provisional diagnosis of acute leukemia was made. However, immunohistochemistry and flow cytometry analysis revealed that the cells presumed to be blasts were in fact rhabdomyosarcoma cells masquerading as leukemia. The mutational landscapes of the primary tumor and the bone marrow metastasis had similar yet distinct profiles. Annotation analysis suggested that the primary and metastatic tumors use alternate mutations to activate the RAS/AKT signaling pathways. In this case, looking beyond the mutational profiling revealed an additional layer of similarity between both the original and metastatic samples, exposing a common and possibly targetable pathway. Application of annotation tools in clinical practice could enable extraction of valuable information from somatic mutational gene panels.