Citrus black rot caused by Alternaria spp. is significant postharvest problem in Iran. The cause of plant disease was originally identified as A. citri by Ellis and Pierce. The genus Alternaria circumscribes considerable morphological diversity and citrus plant disease could also be caused by quite one morphospecies additionally to A. citri. Morphological identification of small-spored Alternaria spp. is difficult. Phylogenetic analysis was performed on 7 small-spored Alternaria isolates from black rotted citrus in Iran using sequence data from an anonymous locus, OPA10-2. Samples were collected from navel oranges in Mazandaran province in the north of Iran. All isolates caused plant disease during a fruit inoculation assay with Navel and Valencia oranges and significant differences were observed between cultivars and among isolates. No association was found between morphological classification and phylogenetic clade.