Abstract Molecular characterisation of four Schistonchus caprifici populations (two from Spain and two from Italy), using the partial 18S, the D2-D3 expansion segments of 28S of ribosomal DNA (rDNA) and the partial mitochondrial gene for cytochrome c oxidase I (mtCOI), is provided. Amplicons from partial mtCOI were analysed using 'Single Strand Conformation Polymorphism' (SSCP) analysis in order to rapidly screen for genetic (haplotypic) variability. SSCP analysis of mtCOI revealed a close relationship between the Spanish and Italian populations with low intra-population variability and only two haplotypes were detected. Mitochondrial COI and ribosomal genes were analysed using Maximum Likelihood and Bayesian inference to reconstruct phylogenetic relationships within S. caprifici and other members of the family Aphelenchoididae. The phylogenetic analysis based on mtCOI showed no geographic variability among Italian, Spanish and Turkish populations. The results of phylogenetic analyses based on the D2-D3 expansion segments of 28S rDNA region and the partial 18S rDNA genes revealed a closer phylogenetic relationship between S. aureus, S. laevigatus, S. virens and S. centerae, whilst S. caprifici and S. guangzhouensis clustered separately. The phylogeny of the genus Schistonchus was well related to some morphological characters, such as position of excretory pore, presence/absence of labial disc and number and position of caudal papillae. The monophyly of the genus Schistonchus was rejected by the Shimodaira-Hasegawa test based on tree topologies.