Tomato (Solanum lycopersicum) is acknowledged worldwide as one of the major vegetable crops, as is the case in Iraq. This research in 2024 was designed to recognize the species of Root-Knot Nematode (RKN) in central Iraq, assess its distribution, and study the level of susceptibility of 5 tomato varieties (SPEEDY, GS-12, SUPER LUX, TALA, and JUDIVIS). Since there is a threat of chemical nematicides, a greenhouse study was performed to evaluate other control methods, such as the use of organic fertilizers and the extract of nettles (Urtica dioica). Root-knot nematode (RKN) species consisting of Meloidogyne incognita, M. arenaria, and M. javanica were found in Baghdad, while only M. incognita was found in Babil. Molecular identification confirmed M. javanica in both Baghdad and Babil. Among the tomato cultivars, GS-12, TALA, JUDIVIS, and SUPER LUX, the Root-Knot Nematode (RKN) galling index and the degree of susceptibility in root galling were significantly different. GS-12 was the most susceptible and had a galling index of 3.60, then TALA had a galling index of 3.20, and JUDIVIS had a galling index of 2.40. SUPER LUX had high resistance with an index of 2.20. GS-12 also had the most nematode reproduction with 144 juveniles + eggs/100 cm³ Soil, while TALA and SPEEDY had 81, which were much lower. Plant growth also differed in the varieties. TALA had the highest increase in stem height, which was 38.5 cm, while SUPER LUX had the highest fresh Weight of 7.0 g. The nematode-fungal infection of the plants was significantly lower in the alternative treatments. The most efficacious of the options provided was Urtica dioica (galling index 2.0), followed by sheep manure (2.2) and then cattle manure (2.4). Listed poultry manure was still less efficacious (3.2) and did not vary statistically from the control group (3.6). These results illustrate the potential for cultivar-specific targeting of RKNs and underscore the potential of both Urtica dioica and organic-based fertilizers for sustainable management of tomatoes. This study provided advances in the discipline of Plant Sciences, focusing on the integration of phytopathology and the science of protective agriculture.