Glochinema spinithorni sp. nov. is described from muddy, bathyal sediments of the oxygen minimum zone (OMZ) of the north eastern Pacific Ocean off Baja California. It is characterized by a rather large body length (over 1 mm), a large number of body rings (242-282), sexual dimorphism in the number and position of pharyngeal thorns near the head region, cuticular ornamentation with numerous hairy spines and two sets of stronger spines ventrally in the anterior body half, mid-sized spiral amphids, and by the number and arrangement of ambulatory setae and long spicules (over 100 μm). The finding of a second OMZ Glochinema species with similar morphological characteristics supports the presumption that OMZs function as isolated habitats promoting endemism at low taxonomic levels. Results of phylogenetic analyses at the species level restricted to the Glochinematinae and Keratonematinae suggest that both OMZ species form a monophyletic group. An attempt was made to recognize phylogenetic relationships at species level within the family. The phylogenetic analyses were based upon a data matrix of 96 ingroup taxa and 25 characters. The results support the monophyly of the genera Leptepsilonema, Metepsilonema, Perepsilonema and Polkepsilonema (with or without Pternepsilonema).