Hematologic malignancies, particularly lymphoma and leukemia, are a diverse group of diseases with a myriad of different presentations. Although the diagnosis of these diseases can be straightforward, there are many cases in which the diagnosis is difficult to establish with conventional methods. Molecular diagnostic testing to identify oncogenes and clonal lymphocyte populations can aid in resolving ambiguous cases, and several of these tests are routinely available for canine patients. Sensitive polymerase chain reaction-based methods are also useful for answering a variety of research questions. Here, detection of mutations of the c-kit gene in mast cell tumors, the bcr-abl fusion gene in myelogenous leukemias, and clonality of lymphocyte populations for the diagnosis and monitoring of lymphoma and leukemia are discussed.