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<i>Phyllosticta citricarpa</i> is the causal agent of citrus black spot (CBS), a disease first reported in Australia in 1895. In 2010, CBS was found in Southwest Florida and has continued to spread in this region. We have previously determined by sequence analysis that individual isolates of <i>P. citricarpa</i> contain either the MAT1-1 or MAT1-2 mating-type idiomorph. From this we surmise that <i>P. citricarpa</i> is a heterothallic fungus requiring compatible mating-types to generate airborne ascospores. In this project, locus specific primers for MAT1-1-1 and MAT1-2-1 were designed to screen the mating-type of 113 isolates from Florida and 26 from Australia. Only MAT1-2-1 isolates were found in Florida while stains from Australia display a 1:1 ratio of both the mating-types. Based on this screen, we hypothesized that the Floridian population is clonal. To test this hypothesis, seven polymorphic microsatellite/simple sequence repeat (SSR) markers were designed to establish multi-locus genotypes (MLGs) for Floridian and Australian populations. With SSR genotyping, 11 MLGs were revealed in 24 Australian isolates, but only one MLG was present in 72 Floridian isolates representing isolates from multiple groves collected over four years. This data suggests that the <i>P. citricarpa</i> population in Florida is a clonal asexually reproducing population derived from a limited introduction and the disease management strategies should be focused on controlling production and movement of conidia.