Alien woody species are one of the most succesful invaders in the world, despite of these species are frequently used for afforestations in several regions such as semi-arid lands. Shrubs and trees can form important patches, creating microhabitats in the open area of arid lands. These vegetations have unique species composition and coexistence of species modes. However, effects of solitary conifer species on the understory vegetation are lacking. This study evaluated the effects of the solitary native and invasive conifer species, Juniperus communis and Pinus nigra on the beta diversity of the surrounding vegetations. To determine the impacts of the conifer invasion on species richness and structure in this habitat, a field study was conducted in Pannonic dry sand grassland in the growing season of 2018. The presence of plant and lichen species were recorded in the vegetation around each six selected solitary conifers. 26 m long circular transects, which consist of 520 units of 5 cm × 5 cm contiguous microquadrats were used for beta diversity estimation. Two information theory models were calculated the baseline transect data, in order to describing the fine-scale spatial structure of each understorey community. The results showed significant differences (p ≤ 0.05) between the two types of understory vegetation functions and these parameters. Our result show, the native conifer J. communis creates a more complex, highly organized microhabitats compared to the invasive, P. nigra. Thus, can conclude that native conifer species has positive effect on the beta diversity of understorey vegetation. Based on our study, the removal of the invasive woody species is required in order to sustain diversity of these habitat and reducing the risk of the introduction of other alien species.