Crepidorhopalon perennis is a metallophyte critically endangered by mining activities and currently known from only one site on copper-rich soils in Katanga (Dem. Rep. Congo). It is closely related to the annual C. tenuis, also a rare metallophyte, but with a broader geographical range. We investigated the variation in morphometric traits and ecological niches (based on edaphic conditions and pollinator assemblages) of C. perennis and C. tenuis, to evaluate the risk of inter-specific competition, and their potential for hybridization to ascertain if C. perennis might be at risk of genetic swamping by its more widespread congener. We examined whether species were found under sympatric or parapatric settings with opportunity for hybridization (or gene exchange). Such knowledge is essential for implementing restoration management protocols, including the introduction of C. perennis into substitution sites where C. tenuis might be already present. Fourteen morphological characters and 11 soil variables were measured and visiting pollinator species were identified at the site where the two species co-occur. Our results show that the two species can be distinguished based on their morphological traits, show niche overlap based on edaphic properties, and share the same pollinator assemblage. In addition, no morphologically intermediate individuals could be detected, suggesting no hybridization, and that the two species may be reproductively isolated. We conclude that C. perennis conservation and restoration operations can be realized in substitution sites where C. tenuis may be present, with the need, however, to evaluate the potential effect of sharing a pollinator assemblage on reproductive success of both species.