This study aims to clarify the taxonomic doubts, which have varied over the centuries, on the only two endemic species of the genus Pimpinella growing in Italy: P. anisoides and P. gussonei. For this purpose, the main carpological characters of the two species were examined, analyzing the external morphological traits and their cross-sections. Fourteen morphological traits were identified, obtaining datasets for the two groups using 40 mericarps (20 per species). The obtained measurements were subjected to statistical analysis (MANOVA and PCA). Our results highlight that at least 10 of the 14 morphological traits analyzed support the distinction between P. anisoides and P. gussonei. In particular, the following carpological characters are very significant ways to distinguish between the two species: monocarp width and length (Mw, Ml), monocarp length from base to maximum width (Mm), stylopodium width and length (Sw, Sl), length/width ratio (l/w) and cross-section area (CSa). In particular, the fruit of P. anisoides is larger (Mw 1.61 ± 0.10 mm) than that of P. gussonei (Mw 1.27 ± 0.13 mm), the mericarps of the first species are longer (Ml 3.14 ± 0.32 vs. 2.26 ± 0.18 mm) and the cross-section area (CSa) of P. gussonei is larger (0.92 ± 0.19 mm) than that of P. anisoides (0.69 ± 0.12 mm). The results also highlight the importance of the morphological traits of the carpological structures for the specific discrimination of similar species. The findings of this study contribute to an evaluation of the taxonomic significance of this species within the genus Pimpinella, and also provide valuable information for the conservation of these two endemic species.