The coffee corky-root disease associated with root-knot nematode infection is a major concern for coffee production in Mexico, particularly in the Veracruz State where substantial losses from Coffea arabica plantations are reported annually due to this disease. Previous studies based on perineal patterns of Meloidogyne females identified M. incognita as the species responsible for coffee corky root disease in this state. Populations of Meloidogyne were collected from coffee plants with corky root symptoms and from intercropped banana plants, when present, in eight sites distributed through the major coffee growing region of Veracruz State. These populations were characterized by multiplex PCR using sequence-characterized amplified region (SCAR) markers for the three major coffee Meloidogyne species in Latin America: M. exigua, M. incognita and M. paranaensis. M. paranaensis was the only species present on all eight coffee samples and is reported here for the first time in Mexico. Consequently, the coffee industry in Mexico should focus more attention to this very destructive root-knot nematode, particularly at the prophylactic level to avoid its dissemination via nursery seedlings. Additionally, M. paranaensis was found in the five samples of intercropped Musa AAA and AA plants suggesting that this crop is a good host and a potentially important way of dispersal of this very pathogenic root-knot nematode since banana suckers are frequently used by growers for plantation renovations. Additionally, M. incognita was detected on Musa AAA and AA plants in three of the five studied sites with intercropped banana but never on the coffee plants even those sampled nearby banana plants.