Tamarillo (Solanum betaceum Bosh) is a plant from the highland tropics of great importance in the fruit agroindustry of Colombia. In recent years, there has been a dramatic decrease in the local tamarillo fruit production as a result of an emerging disease caused by the potyvirus Tamarillo leaf malformation virus (TaLMV). Symptoms of TaLMV infection include rugose mosaics, severe leaf deformation, defoliation and reduction in plant longevity. In this work, we present a second genome sequence of TaLMV obtained from a tamarillo-growing region in northern Antioquia (Colombia). This genome was compared with a previously sequenced isolate from La Union in eastern Antioquia; this information was used to design specific primers targeting the CP and CI regions of the TaLMV. These primer sets will be useful in future epidemiological studies, seed certification schemes and genetic improvement programmes using real-time RT-PCR (RT-qPCR) and/or RT-PCR.