A total of 1,294 goodeid fish representing 35 species collected from 51 localities in Mexico was examined for adult intestinal helminths. Sampling was conducted between September 2001 and December 2004. Ten helminth species were collected (4 digeneans, 2 cestodes, and 4 nematodes). Allocreadium lobatum and Proteocephalus longicollis are reported for the first time in Mexico. The geographic and host range of Allocreadium mexicanum is extended to include new host species within Goodeinae in the Mezquital basin. Margotrema bravoae was found mainly in the Lerma-Santiago River basin and sparsely in the Balsas River, and Margotrema guillerminae was only found in the Western basins related to the Mesa Central. Proteocephalus longicollis was found in 1 host and 1 location. Rhabdochona lichtenfelsi was the most prevalent and abundant helminth in collections from the freshwater basins of Lerma-Santiago and Pánuco river systems. It is considered as the only nematode species of goodeids endemic to both basins. Rhabdochona ahuehuellensis was found mainly in the Balsas, in the Western Basins supposed to have been formerly related in geological time to the Balsas, and in the Panuco basin. Margotrema bravoae, M. guillerminae, R. ahuehuellensis, and R. lichtenfelsi are considered to be the core species of the helminth communities of Goodeinae. Two exotic helminths, Bothriocephalus acheilognathi and Pseudocapillaria tomentosa, are reported from new hosts and locations. Overall, 29 new host and 48 new locality records are reported for endohelminths of goodeid fishes in Mexico. Distribution of Margotrema spp. is congruent with a vicariant origin that closely mirrors the phylogeny of the Goodeidae whereas Rhabdochona spp. does not, indicating it has multiple host and biogeographical origins within the Americas.