[Aim] Severe root-knot nematode disease occurs during the seedling stage of direct seeding rice in Jiangjing Town, Fuqing City and Tanxi Town, Fu'an City, Fujian Province. This study was performed to identify the species of Meloidogyne, based on morphological and molecular characteristics and to provide a insights for disease prevention and control. [Method] Morphological characteristics of the nematode were determined, and its rDNA ITS was sequenced. Phylogenetic trees were constructed based on the rDNA-ITS sequences using Bayesian and maximum likelihood analyses. The population was also examined using M. graminicola-specific primers. [Result] The morphological characteristics of female, male, and second-stage juveniles (J2) matched the original description of M. graminicola. The rDNA-ITS sequence was 576 bp long, and BLAST analysis suggested > 99% similarity to other available M. graminicola sequences in GenBank. Phylogenetic analyses revealed that this nematode clustered with M. graminicola. Species identity was further confirmed using M. graminicola-specific primers. [Conclusion] In the study, the species of rice root-knot nematode parasitizing direct seeding rice in Fujian Province was confirmed as M. graminicola based on morphological and molecular data. The rice root-knot nematode disease caused by M. graminicola was first found in small scale rice field in Zhenghe County, Fujian Province in 2011, and has not been found again in other rice paddy fields in Fujian Province. The research has found M. graminicola has caused severe disease on direct seeding rice for the first time in Fujian Province. With the promotion of direct seeding rice, the disease caused by M. graminicola has become a major problem restricting direct seeding rice production and should thus receive sufficient attention.