To elucidate relationships among Alternaria, Ulocladium, and Stemphylium species, nuclear internal transcribed spacer (ITS) and
mitochondrial small subunit (SSU) ribosomal DNA (rDNA) sequences from 18 Alternaria, four Ulocladium and four Stemphylium spp.
were determined and compared. Phylogenetic analysis of the ITS and SSU rDNA sequences, performed by the neighbour joining
and maximum parsimony methods, revealed that the Stemphylium spp. were phylogenetically distinct from the Alternaria and
Ulocladium spp. Most Alternaria spp. and the Ulocladium spp. were placed together in a large Alternaria/Ulocladium clade. Within this
large clade, the Alternaria spp. clustered into several distinct species-clades, most of which correlated with species-groups previously
established based upon morphological characteristics. The Ulocladium spp. were placed into two species-clades, each of which also
included Alternaria spp. A. longissima was distantly related to the other Alternaria spp., as well as the Ulocladium and Stemphylium
spp. Based upon ITS and nuclear 18S rDNA sequence identities, A. longissima was most closely related to Leptosphaeria.