Resistant rice varieties are considered to be a potential alternative for controlling the plant-parasitic nematode Meloidogyne graminicola in the field due to their joint economic and environmental sustainability features. However, the emergence of virulent pathogen forms threatens natural resistance durability. In this study, we isolated a virulent M. graminicola population from a naturally infested field in Cambodia that overcomes the resistance of the Oryza sativa Zhonghua 11 rice variety. We used molecular (internal transcribed spacer of rDNA and mitochondrial markers) and morphological approaches to unequivocally identify and confirm the species identification. Few intraspecific variabilities in traits between the virulent pathotype and several avirulent pathotypes were found. Remarkably, histological analysis showed the absence of a hypersensitive response (HR) on root cells surrounding the nematode in the "virulent pathotype-Zhonghua 11" interaction. In addition, the virulent pathotype reproduced to a significant extent in two other Oryza sativa varieties known to be resistant to M. graminicola. However, this virulent population was unable to overcome the previously described resistance in three Oryza glaberrima varieties. We concluded that the virulent M. graminicola pathotype isolated in this study could compromise rice breeding programs based on the sole use of known resistant O. sativa gene pools. The identification of this virulent pathotype should provide the genetic resources needed to study the molecular mechanisms that may enable M. graminicola to bypass HR resistance.