Abstract Porcine circovirus 3 ( PCV 3) was recently discovered and is a new species of the genus circovirus. Clinically, it is associated with absence of symptoms or with different clinical syndromes. It has been reported in different countries of America, Europe and Asia. Last year, in Colombia, some farms have reported symptoms similar to those caused by PCV 2. Samples were taken from two farms located in the centre of the country, and the presence of PCV 3 was determined by PCR in two samples, one from a pool of sera and another from mesenteric lymph node. The strains were fully sequenced (GenBank accession numbers MH 327784 and MH 327785) and classified into subgroups a1 and a2. According to this classification and its analysis, strain a2 is located within the group called “Linker” that may be evolving towards group “b”. In addition to the above, the two Colombian strains were compared with 104 strains reported in the GenBank database. The phylogenetic tree obtained grouped according to the classification of subgroups a1, a2, b1 and b2. It was found that subgroups a1 and a2 were well grouped when comparing whole genomes, but the same was not observed with the strains of group “b”. In the latter, no subgroups were evidenced when comparing complete genomes. It is suggested that a new classification of PCV 3 subgroups should be proposed, based on whole genome sequences. This is the first report of PCV 3 in Colombia and its complete genome sequence.