Hemicriconemoides mangiferae and H. litchi, which have been considered as junior synonyms of H. strictathecatus, are morphologically similar, making identification difficult. In the present study, six populations of Hemicriconemoides spp. were collected from mango and litchi in Taiwan and were differentiated based on morphometrics and molecular characteristics. By comparing morphometric data from females and males, three populations collected from mango were identified as H. mangiferae and another three populations from litchi were identified as H. litchi. According to SEM, both of the H. mangiferae and H. litchi males had an areolated lateral field with four incisures; caudal alae were not found. The internal transcribed spacer (ITS) sequences of ribosomal DNA (rDNA) from these nematode populations were sequenced and aligned. The sequence identity of the ITS region was 89-95% between H. mangiferae and H. litchi populations, suggesting rDNA sequence divergence could be a taxonomic aid for species differentiation. Since H. mangiferae and H. litchi are closely related to H. strictathecatus, more rDNA sequence information could be valuable to deal with molecular phylogenetic relationships of these species in depth.