Six isolates of Australian Aphelenchoidoidea, viz., Laimaphelenchus preissii from native coniferous Callitris preissii trees, L. australis from the common pine plantation trees of Pinus radiata and P. pinaster and L. heidelbergi and two morphospecies of Aphelenchoides (H1 and K1) and Cryptaphelenchus sp. (K2) from diseased P. radiata trees, were studied using light microscopy, scanning electron microscopy and phylogenetic analyses of nearly full length sequences of SSU, D2/D3 expansion segments of LSU rDNA and a fragment of cytochrome oxidase subunit I (COI). Bayesian phylogenetic analyses of SSU, LSU and COI of the six nematode species revealed that none of these Australian aphelenchoidoids was inferred to be closely related to Bursaphelenchus. The selected isolates of Aphelenchoides and Laimaphelenchus used in this study were paraphyletic in all molecular analyses. Cryptaphelenchus sp. (K2) was inferred to be sister to Seinura with SSU sequences.