The objective of this work was to study the level of variation of PMTV isolates from Colombian potato crops through 2010 and 2011. Genes encoding for the viral coat protein (CP, ARN 2) and the Triple Gene Block (TGB2, ARN 3) were sequenced from PMTV isolates obtained in the provinces of Antioquia, Boyacá, Cundinamarca y Nariño. Additionally, RNA 2 and RNA 3 from two isolates were almost sequenced to completion (>83%). Phylogenetic analysis based on the CP sequence revealed the presences of two clades. The first clade included PMTV reference strains from all over the world and 19 Colombian isolates used in this study. The second class grouped only Colombian isolates and shared less than 76% identity with clade 1, suggesting a new pomovirus species. Complete genome sequencing is required to confirm this hypothesis. Phylogenetic analysis using the TGB2 gene grouped all sequences in a single clade. Sequence analysis of segments 2 and 3 of the viral genomes revealed >94% sequence identity with PMTV isolates from Czech Republic and Sweden. These findings will be helpful in the development of diagnostic tools for PMTV in the Andes in order to support tuber-seed certification and genetic improvement programs.