In this study, the distribution and characterization of root-knot nematode species collected from intensively vegetable growing areas of Lakes Region were determined by morphological, molecular and North Carolina Differential Host Test between September 2014 and December 2015. A total of 160 samples were collected and 83 (51.8%) were found to be infested with root-knot nematodes. Each population was cultured from a single egg mass taken from galled roots and multiplied on the susceptible tomato cv. Tueza F1. Sixty-eight populations were morphologically identified based on perineal patterns and morphometrics of second stage juveniles, and molecularly determined using species specific primers. Of the 68 populations analyzed, 66 were identified as Meloidogyne incognita (25), M. hapla (22), M. javanica (18) and M. arenaria (1), and two populations were not identified. The incidence of M. incognita, M. hapla, M. javanica and M. arenaria was 36.7, 32.3, 36.5 and 1.5%, respectively. According to the differential host test, M. incognita races 2, 4 and 6 and M. javanica races 1 and 3 were determined. This was the first detection of Meloidogyne javanica race 3 in Turkey. Eighty four percent of the M. incognita populations were found in microclimatic areas with altitudes of up to 800 m, while 16% were found at altitudes between 800 and 1035 m. Some M. javanica populations (17%) were found in high plateau fields in this region, whereas most (83%) were found in lowlands. In contrast, the large majority of M. hapla populations (91%) of were found in cool, high altitude areas with sandy soils, whereas only 9% of M. hapla populations were in lowlands.