Understanding the genetic structure of natural enemies is an important step to develop efficient biocontrol programs. The ladybird Iberorhyzobius rondensis Eizaguirre (Coleoptera: Coccinellidae) from the Iberian Peninsula, is a specialized predator and potential biological control of Matsucoccus feytaudi Ducasse (Hemiptera: Matsucoccidae), an invasive alien species in Southeastern France and Italy. M. feytaudi is specialized on Pinus pinaster Aiton. The beetle is also restricted to this habitat. Genetic structure of I. rondensis populations was analysed with the barcode region (COI). It revealed two main refugia areas for the beetle in Iberian Peninsula. Comparative phylogeography of the three trophic levels, plant-herbivore-predator, is discussed. Similar population structure was found for the prey and to some extent for the pine. Indications are given on where to collect the beetles for their use in biocontrol of M. feytaudi, in order to obtain the highest genetic diversity and match with the origin of the invasive prey.