The complete nucleotide sequence of pepper huasteco geminivirus (PHV) isolated in Northern Mexico was determined. The PHV genome consists of two circular ssDNA molecules of 2631 bases (PHV A) and 2589 bases (PHV B). PHV has a genome organization typical of a bipartite geminivirus with four open reading frames (ORFs) (AR1, AL1, AL2 and AL3) in component A and two (BR1 and BL1) in component B. An unexpected ORF was found in the complementary sense strand of PHV A. This ORF, termed AL5, is found entirely inside, but in the opposite orientation to AR1 (encoding the coat protein). AL5 shows some homology to equivalent but smaller ORFs predicted in other geminiviruses. Phylogeny trees based on pairwise comparisons of AR1, AL2, AL3, BL1 and BR1 predicted proteins placed PHV among the western hemisphere geminiviruses. A phylogeny tree based on AL1 (replicase-encoding ORF), on the other hand, placed PHV with eastern hemisphere geminiviruses, i.e. African cassava mosaic virus and the Sardinia and Israel isolates of tomato yellow leaf curl virus. Possible mechanisms for the 'hybrid or transition nature' of PHV are discussed.