Scirtothrips aurantii is a generalist horticultural pest in its native African range and recently established quite widely in Australia on the invasive succulent weed Bryophyllum delagoense. Paradoxically, this thrips is not polyphagous in its incursive range. The issue is principally one of quarantine. Will the thrips in Australia shift, perhaps adaptively, to citrus, and should the primary focus be on containment around Australian citrus, or does the real quarantine risk exist offshore with thrips present on citrus in Africa? We examined the phylogenetic relationships between Bryophyllum-associated thrips populations in Australia and populations sampled from various host plant species in South Africa (including Bryophyllum) using both CO1 and 28s markers. Eight variable microsatellite markers were developed to assess the extent of gene flow between the thrips on different hosts in South Africa. The COI phylogeny resolved S. aurantii into three distinct clades with samples collected from B. delagoense in South Africa and Australia representing a single clade, a second clade associated with Gloriosa lilies and the third with horticultural hosts. The microsatellite analysis confirmed that the populations associated with citrus and Bryophyllum do not hybridize with one another in sympatry. We conclude that the citrus-damaging thrips are not currently present in Australia and remain a serious quarantine concern in relation to Australian horticulture.