Partial sequence comparisons of mitochondrial small subunit rDNA (mt SSU rDNA) were used to examine taxonomic and evolutionary relationships among seven Penicillium species: two monoverticillate species, two biverticillate species, and three terverticillate species. Amplified fragments of mt SSU rDNA highly varied among seven species in size, suggesting the existence of multiple insertions or deletions in the region. A phylogenetic tree was constructed by exhaustive search of parsimony analysis. The phylogenetic tree distinguished two statistically supported monophyletic groups, one for two monoverticillate species and the other for three terverticillate species and one biverticillate species, P. vulpinum. The phylogenetic relationship of P. waksmanii, the biverticillate species, was not clear.