The Capparaceae are a family of plants associated mainly with dry areas, which have produced climatic constraints and a limited geographic distribution. This family is considered endemic in the Neotropical seasonally dry forest (NSDF) and, therefore, a model to analyse the NSDF biogeography. We conducted a track analysis of Neotropical species of Capparaceae to identify generalised tracks that recover ancestral biotas of NSDF nuclei, employing 7602 data points for 104 species. Individual tracks were obtained using Prim’s algorithm and generalised tracks were identified using parsimony analysis of endemicity with progressive character elimination. We found six generalised tracks and four panbiogeographic nodes mainly located in the NSDF. Generalised tracks recovered the ancestral biotas of NSDF distributed among the central Andean coast, central inter-Andean valleys (Ecuador), Tarapoto–Quillabamba, Apurimac–Mantaro (Peru) and Piedmont (Bolivia) NSDF nuclei. Also, the pattern of distribution of Capparaceae recovered old connections between northern South America and the inter-Andean valleys. However, we also found generalised tracks located over the Isthmus of Panama and Amazonian–Magdalena valley moist forest, suggesting that the distribution pattern in this family was influenced not only by NSDF climatic constraints, but also by geological events such as the emergence of the Isthmus and Andean uplift.