Abstract A standardised methodology has been used to define genotypes based on pairwise sequence comparisons (PASC). PASC is a widely accepted method in virus taxonomy, which is based on the histogram of pairwised differences among sequences. Recently, Zhang et al. (2013) concluded that the average p-distance of duck circovirus (DuCV) between genotypes 1 and 2 was 0.170, and subtype distance thresholds were 0.032 in DuCV-1 and 0.018 in DuCV-2, respectively. However, there might be some concerns on the methodology application to define the genotype of DuCV. Taking into account the concerns mentioned above, our authors conducted the PASC analyses of 54 capsid gene (ORF2) and genomic sequences including all the sequences from Zhang et al. (2013). Our results confirmed the existence of two DuCV genotypes (1 and 2) and, we suggest that DuCV ORF2 and genomic distance genotype thresholds were 0.061 and 0.038, respectively.