We address the systematics of Bruchus seed-beetles through the use of a geometric morphometric outline approach, namely elliptic Fourier analysis. We found that a previously neglected genitalic structure, the ventral plate, provides new evidence in the discussion of taxonomic issues raised by recent molecular studies. Three methods of hierarchical clustering allow investigation of the phylogenetic relationships of the key species that cause the paraphyly of two species groups in recent molecular studies. The resulting reconstructions reveal the phylogenetic usefulness of the structure of interest in recovering consistent relationships of Bruchus. Our analyses support the monophyly of the species group whose paraphyletic status was weakly supported by statistical tests in molecular analyses. Our results agree with those molecular and morphological studies that indicate, with relatively strong support, the paraphyletic status of the other species group. We highlight the need to reappraise the use of neglected or presumably uninformative (in traditional morphometrics) morphological characters with geometric morphometrics methods. In addition, we assess the utility of the combination of morphometric descriptors with other sources of phylogenetic information by analysing together an extant molecular dataset and matrix representations based on the results of the elliptic Fourier analyses (to our knowledge our study is the first to investigate such a combination of datasets within a Bayesian framework). Combining morphometric descriptors with other information can improve phylogenetic reconstructions, as suggested by the results of the corresponding analyses we performed using a published molecular dataset.