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Background  Understanding genomic and phenotypic diversity among cryptic pest taxa has important implications for the management of pests and diseases. The diamondback moth,  Plutella xylostella  L., has been intensively studied due to its ability to evolve insecticide resistance and status as the world’s most destructive pest of brassicaceous crops. The surprise discovery of a cryptic species endemic to Australia,  Plutella australiana  Landry & Hebert, raised questions regarding the distribution, ecological traits and pest status of the two species, the capacity for gene flow and whether specific management was required. Here, we collected  Plutella  from wild and cultivated brassicaceous plants from 75 locations throughout Australia and screened 1447 individuals to identify mtDNA lineages and  Wolbachia  infections. We genotyped genome-wide SNP markers using RADseq in coexisting populations of each species. In addition, we assessed reproductive compatibility in crossing experiments and insecticide susceptibility phenotypes using bioassays.    Results  The two  Plutella  species coexisted on wild brassicas and canola crops, but only 10% of  Plutella  individuals were  P. australiana . This species was not found on commercial  Brassica  vegetable crops, which are routinely sprayed with insecticides. Bioassays found that  P. australiana  was 19-306 fold more susceptible to four commonly-used insecticides than  P. xylostella . Laboratory crosses revealed that reproductive isolation was incomplete but directionally asymmetric between the species. However, genome-wide nuclear SNPs revealed striking differences in genetic diversity and strong population structure between coexisting wild populations of each species. Nuclear diversity was 1.5-fold higher in  P. australiana , yet both species showed limited variation in mtDNA. Infection with a single  Wolbachia  subgroup B strain was fixed in  P. australiana , suggesting that a selective sweep contributed to low mtDNA diversity, while a subgroup A strain infected just 1.5% of  P. xylostella .    Conclusions  Despite sympatric distributions and the capacity to hybridize, strong genomic and phenotypic divergence exists between these  Plutella  species that is consistent with contrasting colonization histories and reproductive isolation after secondary contact. Although  P. australiana  is a potential pest of brassicaceous crops, it is of secondary importance to  P. xylostella .    Electronic supplementary material  The online version of this article (10.1186/s12862-018-1183-4) contains supplementary material, which is available to authorized users.

Cryptic Plutella species show deep divergence despite the capacity to hybridize