Cestodes of the genus Taenia occur as adult tapeworms in the small intestine of carnivorous definitive hosts and are transmitted to particular mammalian intermediate hosts, in which they develop as fluid-filled larvae in tissues, causing the disease cysticercosis or coenuriasis. A number of species are of medical importance and/or cause losses to the meat and livestock industry mainly due to the condemnation of infected muscle and offal. The control of taeniid cestodes relies upon epidemiological data, including the precise identification and characterization of the causative agents. Traditional, phenetic techniques have limitations for specific diagnosis. Although there has been progress in the establishment of molecular tools, there has been relatively limited application of mutation scanning approaches to species of Taenia. In the present article, we briefly review key genetic markers used for the specific identification of taeniids and tools for the analysis of genetic variation within and among populations and the diagnosis of taeniasis and cysticercosis/coenuriasis. We also discuss the advantages and disadvantages of selected techniques and emphasize the benefits of utilizing mutation scanning-based approaches in achieving detailed insights into the population genetics and epidemiology of Taenia species.