Allochthonous alga Caulerpa taxifolia (Vahl) C. Agardh has been present in the Mediterranean Sea for over thirty years. Different types of negative impacts on species and entire communities have been well documented; however, studies of its impact on meiofauna are scarce. The aim of this study was to investigate the structure of meiofauna in the area impacted by the invasive alga, C. taxifolia, in the Stari Grad Bay (43.1833°N, 16.5838°E), Adriatic Sea, in December 2008 (autumn) and June 2009 (spring). To establish the nature of the impact on meiofauna inhabiting the sediment of the studied area, we compared the structure of meiofauna inhabiting bare sediments with the structure of meiofauna inhabiting sediments beneath the autochthonous seagrass (Posidonia oceanica (L.) Delile) and invasive alga (C. taxifolia). Furthermore, comparisons between epibiontic meiofauna inhabiting alga and seagrass were made. Multivariate statistical analysis revealed differences in the composition of meiofaunal assemblages inhabiting unvegetated and vegetated sediments (P. oceanica and C. taxifolia), during spring. However, no significant differences in composition of meiofauna in sediments inhabited by the invasive alga and those inhabited by the native seagrass were detected. However, the observed impact of C. taxifolia on meiofauna in sediment could be characterized as negative, due to the observed decrease of meiofaunal density in sediment inhabited by the aforementioned alga. Considering the epibiontic meiofauna, our study showed that P. oceanica increases the meiofaunal density in the Stari Grad Bay ten times as much as the allochthonous, invasive C. taxifolia. However, the biodiversity of higher taxonomic categories has not been affected.