This study tested floristic and structural links existing in seasonally dry tropical forests (SDTFs) fragments on carbonate rocky outcrops among three (3) phytogeographic domains (Atlantic, Caatinga and Cerrado) in Brazil. Although included in large-scale SDTFs studies, these disjunctions under limestone are in part poorly understood and little is known about the diversity patterns in these areas. Thus, eight (8) fragments were sampled, three (3) from cerrado, two (2) from Atlantic and three (3) from Caatinga for phytosociological surveys and subsequent characterization of the structure and floristic composition. The structure differed from each other among fragments (even on the same substrate) and between the domains. There were greater similarities only between patches and its surrounding vegetation. However, key SDTFS species were shared among domains with high Coverage Value (CV). Climatic variables were essential in fragments differentiation by seasonality, separating Cerrado and Caatinga domains (higher precipitation seasonality and higher temperatures) against Atlantic domain by milder climate and higher altitudes. Thus, sampled patches presented metacommunity characteristics, with great floristic and structural dissimilarity conditioned mainly by climatic factors and by the influence of adjacent phytogeographic vegetation domains.