Rhizosphere communities of the invasive narrow-leaved ragwort (Senecio inaequidens) and the native tansy ragwort (Jacobaea vulgaris) co-occurring in three semi-natural habitats are compared. For both species, two life stages were taken into consideration. Bacterial and fungal communities at a high taxonomic level and bacterivorous and fungivorous nematode communities were measured using qPCR assays. At high taxonomic level, no differences were observed in fungal rhizosphere communities between native and non-native ragwort species. The impact of plant developmental stages on rhizosphere biota was prominent and this impact was similar in nature for both native and non-native ragwort species. In this manuscript it is shown that closely related native and exotic plant species may cause differential shifts at high taxonomic level in the microbial rhizosphere community, and these changes are reflected in the next trophic level.