Metaperipatus inae sp. nov. (Onychophora: Peripatopsidae) from Chile is described and compared with the previously monotypic M. blainvillei by light, fluorescence, and scanning and transmission electron microscopy. The new species is distinguished from M. blainvillei by having (1) fixed number of legs in both sexes, (2) a characteristic color pattern of the integument, and (3) a larger body size. The structure of the ovaries in both species is different from that in other onychophorans. In contrast to other species of Peripatopsidae and South-East Asian Peripatidae, stalked oocytes are lacking. In addition, the absence of a germinal epithelium surrounding a central lumen contrasts with the organization of ovaries in the Neotropical Peripatidae. A distinct separation into a sterile and a fertile ovarian portion suggests that the novel type might be derived from an ovary with stalked oocytes characteristic of the Peripatopsidae and South-East Asian Peripatidae. The seminal receptacles in both members of Metaperipatus are small and either non-functional or short-term stores since they contained no sperm in the investigated females. The mode of sperm transfer is by dermal insemination, with spermatophores deposited on the female’s body. Based on these observations, the evolutionary development of the ovaries and reproductive strategies in Onychophora are discussed. In addition, an identification key of onychophorans from Chile is provided.