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Eight species of fruit flies were found in 5 locations of red guava plantations in District Deli Serdang. Fruit flies were identified morphologically at LIPI. Dendrogram results of Neighbor Joining analysis based on RAPD markers of DNA band characters show the genetic closeness of the eight species divided into 3 clusters. Cluster 1 is B. caudata (Kolam and Namoriam) and B. umbrosa (Kolam, Namoriam and Sei Mencirim); Cluster 2 is B. curcubitae (Sei Beras Sekata), B. caudata (Sei Mencirim and Sei Beras Sekata), B. umbrosa (Sei Beras Sekata), B. carambolae (Sei Mencirim and Sei Beras Sekata), and B. papayae (Kolam, Namoriam, Sei Mencirim and Sei Beras Sekata); and Cluster 3 is B. kinabalu (Kolam), B. carambolae (Sawit Rejo, Kolam and Namoriam), B. tau (Kolam), B. papayae (Sawit Rejo), B. curcubitae (Sawit Rejo, Kolam, Namoriam and Sei Mencirim), B. caudata (Sawit Rejo), B.umbrosa (Sawit Rejo) and B. albistrigata (Kolam).