In Africa, peri-urban vegetable production systems supply perishable vegetables to the rapidly expanding urban centers. These highly intensive systems are characterized by high levels of pests and diseases and an excessive use of synthetic pesticides to reduce their population densities. Root-knot nematodes (RKN) are especially prevalent in these systems but are often not recognized, or diagnosed correctly. The limited ability to accurately identify these pathogens likely results in the inappropriate use and misuse of control measures, such as genetic resistance, crop rotation, or synthetic chemicals. Given the perceived importance of RKN, a species characterization study was conducted in pen-urban vegetable (amaranthus, cabbage, pepper, carrot, cassava, eggplant, okra, tomato) fields and some coffee plantations, in Benin, Kenya, Nigeria, Tanzania and Uganda. Meloidogyne spp. were characterized from 143 field samples using esterase phenotypes (EST) and SCAR markers. Five known species were identified: three phenotypes for M. javanica populations (EST J3, Rm: 1.0, 1.25, 1.4; EST J2a, Rm: 1.0, 1.4; EST J2b, Rm: 1.0, 1.25), two for M. incognita (EST Il, Rm: 1.0; EST 12, Rm: 1.05, 1.0), one for M. arenaria (EST A2, Rm: 1.2, 1.3), one for M. enterolobii (EST E4, Rm: 0.70, 0.75, 0.90, 0.95), one for M. izalcoensis (EST 14 Rm: 0.86, 0.96, 1.24, 1.30) and two unusual esterase phenotypes for two unknown species, named Meloidogyne sp.1 and sp.2. Combinations of species were detected from numerous locations. Genetic diversity was further studied using RAPD primers, by comparing a subset of the sampled populations from Africa and some populations from Brazil and El Salvador. The analysis identified separate clusters of the more common and minor species, with low variability observed for African and American populations. The SCAR markers correctly identified all Meloidogyne species with the exception of M. ethiopica, Meloidogyne sp.1 and Meloidogyne sp.2. For Meloidogyne sp.1, the SCAR markers corresponded wrongly to M. javanica and M. arenaria, and for Meloidogyne sp.2 to M. incognita. This demonstrates the shortcomings of using SCAR markers alone, which can generate erroneous results for RKN species. Further morphological and molecular studies are required to clarify the identity of these two atypical species.