Morphologically similarAphelenchoidesspp. populations extracted from rice and forage grass seeds from different geographical regions in Brazil were morphologically and molecularly characterised. Overall, the populations studied separated into two groups based on morphological and phylogenetic analyses, referred to herein as ‘Group-rice’ and ‘Group-forage’. Bayesian phylogenetic analyses of SSU, LSU and mtCOI regions strongly supported the presence of two dichotomous groups with Group-rice and Group-forage populations genetically similar toA. besseyiandA. fujianensis, respectively. This study reports the presence of a morphologically similar species toA. besseyiassociated with seeds of grasses, but genetically distinct based on three genomic regions, which our results strongly suggest to beA. fujianensis, this being a new geographical record for Brazil. Additional information regarding spicule morphology of maleA. besseyiis also reported.