Root-knot nematodes (RKNs; Meloidogyne spp.) are a major constraint of pepper (Capsicum annuum L.) crops worldwide. In Mexico, Sinaloa State is one of the main producers of pepper; however, there is little information available on the distribution, prevalence, and incidence of RKN on this crop. Identification of RKN species and estimation of the epidemiological factors are important to design its management strategies. A total of 190 RKN samples from Los Mochis, Culiacan, La Cruz, and Escuinapa areas of Sinaloa were collected from pepper plants at production stage under greenhouse conditions, to analyze the distribution, prevalence, and incidence of RKN. Primary identification of RKN species was based on perineal pattern morphology and confirmed by molecular SCAR marker-based identification. RKNs were found in all the surveyed greenhouses of pepper, confirming their absolute distribution and prevalence in this crop. Meloidogyne enterolobii, Meloidogyne incognita, and Meloidogyne javanica were identified in the four areas. Overall incidence of M. enterolobii, M. incognita, M. javanica, and mix of M. enterolobii + M. incognita was 63.7, 11.7, 12.8, and 11.7%, respectively, indicating that RKNs are a serious threat for pepper and other crops in Sinaloa State. This information will enable pepper growers to design and implement an appropriate control for RKN species.