Hypoplastic Myelodysplastic Syndrome (h-MDS) comprises 15% of all MDS and has traditionally been difficult to distinguish from aplastic anemia (AA) by current testing. Accurate differentiation is important because treatment and prognosis differ. Since the publication of the 2008 World Health Organization classification of MDS, next-generation DNA sequencing has discovered novel mutations strongly associated with AA and MDS. Recent research supports the utility of identifying these mutations in the diagnosis and management of MDS; however, use of next-generation sequencing is not yet recommended in guidelines and the study is not routinely performed. We present a case where next-generation sequencing performed on a peripheral blood specimen aided the diagnosis and management of a 74-year-old man with h-MDS. This case adds to the growing body of evidence supporting the utility of next-generation DNA sequencing in the evaluation of MDS and h-MDS, particularly when diagnosis remains unclear after standard testing.