Rotten flowers and fruits of dragon fruit, Hylocereus undatus (Haworth) Britton & Rose, from Loei Province, Thailand, were collected and isolated for possible pathogen(s) causing fruit rot. Rotten flowers habored six main species, Bipolaris cactivora, Cladosporium cucumerinum, Fusarium sp., Alternaria sp. and Colletotrichum gloeosporiodes. From fruits, there were three main fungi, B. cactivora, C. gloeosporiodes and Rhizopus stolonifer. The most frequently isolated species from both rotten flowers and the fruits were B. cactivora. Four representatives isolated from B. cactivora were ascessed for pathogenicity, parasitic fitness aspects including: spore germination time, incubation period, latent period, colonization ability and sporulation ability. The pathogen was confirmed morphologically and molecularly with 100% support from Neighbor-joining method and Baysian analysis, as B. cactivora. A possible disease cycle of the fruit rot disease was proposed to indicate the key infection targets for discussion.