Dragon fruit, a kind of fruit belonging to Hylocereus spp., has brought about interest in China not only due to its important economic value with high contents of nutrients, but also due to the striking tolerance to drought stress. Fifteen morphological traits and 111 Inter-Simple Sequence Repeat (ISSR) markers generated from 16 primers were firstly employed to discriminate 50 accessions recently selected in China, as well as to evaluate their genetic relatedness. According to univariate statistical analysis of morphological traits, high variations were observed between or/and within the wild and cultivated lines. The dendrogram of 50 accessions was constructed based on morphological traits. Taking 7.50 as a threshold, three major clusters could be observed, i.e. the first included nine genotypes, which mainly belonged to wild accessions; the second clusters standing for the red pulp genotypes; the third consisting of the white pulp accessions. Each ISSR primer generated 4–10 obvious DNA bands ranging from 100 bp to 1500 bp, with the average of 6.9 per primer.
