BackgroundThe false codling moth (FCM),Thaumatotibia leucotreta(Meyrick, 1913), is a significant pest of various important economic crops and is a EU quarantine pest. In the last decade the pest has been reported onRosaspp. In this study we determined whether this shift occurred within specific FCM populations across seven eastern sub-Saharan countries or whether the species opportunistically switches to this novel host as it presents itself. To achieve this, we assessed the genetic diversity of complete mitogenomes ofT. leucotretaspecimens intercepted at import and analysed potential linkages with the geographical origin and host species.ResultsGenomic, geographical and host information were integrated into aT. leucotretaNextstrain build which contains 95 complete mitogenomes generated from material intercepted at import between January 2013 and December 2018. Samples represented seven sub-Saharan countries and mitogenomic sequences grouped in six main clades.DiscussionIf host strains of FCM would exist, specialization from a single haplotype towards the novel host is expected. Instead, we find specimens intercepted onRosaspp. in all six clades. The absence of linkage between genotype and host suggests opportunistic expansion to the new host plant. This underlines risks of introducing new plant species to an area as the effect of pests already present on the new plant might be unpredictable with current knowledge.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12862-023-02139-5.