Accurate identification of small-spored Alternaria spp. is challenging because of morphological plasticity under non-standard
conditions and the common misapplication of the name A. alternata to a variety of morphologically distinct taxa. A system used by
some authors of naming phytotoxigenic alternarias as pathotypes of A. alternata has further clouded the meaning and usefulness of
this specific epithet. Two hundred and sixty isolates of small-spored Alternaria, primarily from fruit substrates, were segregated into
morphological groups and then subjected to RAPD-PCR analysis using total genomic DNA and three different primers. When
cultured under defined conditions, the pattern of sporulation observed at 50 × magnification was predictive of genetic relatedness as
determined by cluster analysis of RAPD fragment patterns. In RAPD analyses, morphological groups or species were resolved as
distinct branches of the dendrogram: Alternaria gaisen (= A. kikuchiana, A. alternata Japanese pear pathotype, group 2), A. longipes
(= A. alternata tobacco pathotype, group 5), the ‘tenuissima’ group (group 5), the arborescens group (group 3) and the ‘infectoria’
group (group 6). Isolates in groups for which there were only a few representatives clustered as a branch. Analysis of RAPD
fragment patterns confirmed that when Alternaria isolates are cultured and observed under defined conditions, their phenotypic
plasticity is minimized and valid taxonomic separations can be made upon morphological characteristics. We conclude that A.
alternata, A. gaisen, A. longipes and other small-spored saprotrophic or perthotrophic taxa are recognizable as morphologically distinct
taxa. We suggest that the ‘pathotype’ system of naming small-spored Alternaria taxa confers no predictive value relative to
observable morphological and genetic characters, and should be abandoned.