A new species of the genus Metaxonchium is described from natural habitats in Iran. The new species is characterized by having body length of 2.46-3.12 mm, lip region offset by constriction and 8-11 µm wide, odontostyle fusiform and 10-12 µm long, neck 773-1150 µm long, anterior portion of pharynx bearing a spindle-shaped thickening with valve-like structures inside, both parts of the pharynx separated by a short isthmus-like narrowing, pharyngeal expansion 531-825 µm long and occupying up to three-fourths of total neck length, female genital system monodelphic-opisthodelphic, anterior genital branch reduced to a large uterine sac and a small terminal mass, posterior uterus long and tripartite with an intermediate region bearing apophyses, V = 53-57, caudal region conoid with broadly rounded terminus (24-35 µm, c = 79-105, c' = 0.6-0.9), spicules 92-103 µm long and 7-10 spaced ventromedian supplements, at least two of them within the range of spicules. The taxonomy of the genus Metaxonchium is updated, including a list of its species, a key to their identification and a compendium of their morphometrics. Four species are transferred from Axonchium to Metaxonchium: M. coxi, M. japonicum, M. mizukuboi and M. zealandicum.