Whole-length esophagi of 111 Murrah cross water buffaloes (Bubalus bubalis) were collected in the Kathmandu and Chitwan districts of Nepal from December 2009 to February 2010. Gullet worms showing a typical epithelium-dwelling character were detected in 13 of 53 (24.5%) buffaloes in Kathmandu and in 5 of 58 (8.6%) buffaloes in Chitwan. The worms' morphology and measurements were identical to those of Gongylonema pulchrum Molin, 1857, except for the length of the left spicules relative to the body length. Scanning electron microscopy did not detect any further morphological differences regarding the collected specimen from Nepal compared with G. pulchrum. The ribosomal RNA gene (rDNA), including internal transcribed spacer (ITS) 1 and 2, and a partial region of the cytochrome c oxidase subunit I (COI) of mitochondrial DNA of the worms were characterized and compared with those of G. pulchrum collected from cattle, deer, wild boars, and monkeys in Japan and from cattle in Iran. The 18S, 5.8S, and 28S rDNA nucleotide sequences of the buffalo-collected worms had 99.8% (1,779/1,782), 100% (158/158), and 98.3–98.8% (3,494–3,507/3,551) identities, respectively, with those of G. pulchrum from the other host mammals. The ITS regions exhibited higher variations between the buffalo-collected worms and G. pulchrum from the other host mammals (85–88% identity for ITS1 and 56–80% identity for ITS2). The COI also showed lower identities (89.2–90.2%), although only a single amino acid substitution was noted compared with the majority of G. pulchrum samples collected in Japan. Based on these molecular genetic characters in the rDNA and COI mitochondrial DNA, together with a shorter left spicule length relative to body length, the gullet worms isolated from buffaloes in Nepal might belong to a distinct local or buffalo-preferring population of G. pulchrum, although its geographical distribution on the continent and host specificity remain to be clarified.