Nucleotide sequence variation in the ITS1-5.8S-ITS2 region of nuclear ribosomal DNA and in the trnL-tmF region of cpDNA from 28 specimens of Jubula (Jubulaceae), and two outgroup species, was analyzed using maximum parsimony and maximum likelihood. The molecular topologies supported five to six allopatric taxa in Jubula. Relationships of most of these taxa remain unresolved due to lack of support of many deeper nodes. A principal component analysis indicated a broad overlap of morphological characters of these taxa. Based on the morphological similarities of the Jubula taxa and the observed low sequence variation, a subspecies concept is supported. This comprises the taxa J. hutchinsiae subsp. bogotensis, subsp. hutchinsiae, subsp. japonica, subsp. javanica, and subsp. pennsylvanica. With the exception of J. hutchinsiae subsp. javanica, all taxa are monophyletic. Multiple accessions of the temperate taxa J. hutchinsiae subsp. hutchinsiae and J. hutchinsiae subsp. pennsylvanica exhibit a lower sequence variation than the tropical taxa J. hutchinsiae subsp. bogotensis and J. hutchinsiae subsp. javanica.