The vulnerable Boronia keysii Domin. (Rutaceae; BK) and the rare B. rivularis White. (BR), endemic to the Sunshine Coast region of Queensland, and the more widespread B. safrolifera Cheel. (BS) and B. falcifolia (BF), were studied. The taxonomic distinctiveness between the morphologically similar B. rivularis and its more southern congener B. safrolifera had previously been in question. This study clearly confirmed the long genetic separation of these two species. High levels of reproductive activity (%R) were observed in both of the threatened species (B. keysii: %R = 84; B. rivularis: %R = 66), which were also found to differ fundamentally in response to fire (obligate seed regenerators) from the more widespread species (facultative resprouters). Genetic diversity was not consistently related to rarity since B. keysii (vulnerable; H_e = 0.282) and B. falcifolia (common; H_e = 0.294) had significantly (P < 0.05) higher genetic diversity than did B. rivularis (rare; H_e = 0.155) and B. safrolifera (common; H_e = 0.197). There was no relationship between population differentiation and geographic distribution of species since B. keysii (F_ST = 0.293) and B. safrolifera (F_ST = 0.283) exhibited lower between-population diversity than did B. rivularis (F_ST = 0.360) and B. falcifolia (F_ST = 0.324). The average number of migrants per generation was less than one in all species (N_m = 0.604 for BK; 0.444 for BR; 0.634 for BS; 0.522 for BF). All four species are effectively inbred; however, B. keysii (F = 0.85) and B. falcifolia (F = 0.90) had significantly (P < 0.05) higher levels of inbreeding than did B. rivularis (F = 0.621) and B. safrolifera (F = 0.472), indicating that inbreeding was not determined by conservation status.