The rice root-knot nematode, Meloidogyne graminicola, has been reported in Southeast Asia, China, India, South Africa, USA, Brazil, and other countries. Recent surveys in Southern Brazil showed that M. graminicola was widespread in irrigated rice in Rio Grande do Sul, Santa Catarina and Paraná states, and the presence of a species complex with a predominance of M. graminicola (Est VS1 = G1) and other variants showing similar esterase phenotypes (Est G2 = R2, G3 = R3). Meloidogyne oryzae (Est O1) and M. ottersoni (Est Ot0) were also part of this complex and were recently re-described and detected on rice. The present study provides an integrative taxonomy approach of the typical and atypical populations of M. graminicola on the basis of morphological, morphometric and molecular data. Considering morphological and morphometric features, the two atypical populations (Est G2 and G3) are in close agreement with the description of M. graminicola. Based on the molecular characterisation, populations G1, G2 and G3 were successfully amplified by M. graminicola SCAR markers, although the specificity of these markers was questioned. Phylogenetic relationships complemented and confirmed the other studies. In maximum likelihood analysis of ITS, D2-D3 rRNA and COXII-16S rRNA sequences, all populations of M. graminicola from different esterase phenotypes clustered together with other M. graminicola populations, thus confirming that these enzyme phenotypes (G1, G2 and G3) are related to the same species. A high level of intraspecific variability was detected among all populations, but no correlation between genetic variability and geographic origins occurred.