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The fruit fly  Bactrocera caudata  is a pest species of economic importance in Asia. Its larvae feed on the flowers of Cucurbitaceae such as  Cucurbita moschata . To-date it is distinguished from related species based on morphological characters. Specimens of  B. caudata  from Peninsular Malaysia and Indonesia (Bali and Lombok) were analysed using the partial DNA sequences of cytochrome  c  oxidase subunit I (COI) and 16S rRNA genes. Both gene sequences revealed that  B. caudata  from Peninsular Malaysia was distinctly different from  B. caudata  of Bali and Lombok, without common haplotype between them. Phylogenetic analysis revealed two distinct clades, indicating distinct genetic lineage. The uncorrected ‘p’ distance for COI sequences between  B. caudata  of Malaysia-Thailand-China and  B. caudata  of Bali-Lombok was 5.65%, for 16S sequences from 2.76 to 2.99%, and for combined COI and 16S sequences 4.45 to 4.46%. The ‘p’ values are distinctly different from intraspecific ‘p’ distance (0–0.23%). Both the  B. caudata  lineages are distinctly separated from related species in the subgenus  Zeugodacus  –  B. ascita ,  B. scutellata ,  B. ishigakiensis ,  B. diaphora ,  B. tau ,  B. cucurbitae , and  B. depressa . Molecular phylogenetic analysis indicates that the  B. caudata  lineages are closely related to  B. ascita  sp. B, and form a clade with  B. scutellata ,  B. ishigakiensis ,  B. diaphora  and  B. ascita  sp. A. This study provides additional baseline for the phylogenetic relationships of  Bactrocera  fruit flies of the subgenus  Zeugodacus . Both the COI and 16S genes could be useful markers for the molecular differentiation and phylogenetic analysis of tephritid fruit flies.

Distinct Genetic Lineages of Bactrocera caudata (Insecta: Tephritidae) Revealed by COI and 16S DNA Sequences