Anopheles balabacensis Baisas is important malaria vectors in South- East Asia from Leucosphyrus Group. A lot of research have proved that species consist of more than 2 species. Identical morphology between them often give difficulty to identified, causing misidentification. Molecular technique using biomarker is alternative ways to recognize both interspecific and intraspecific variation. Phylogenetic trees reconstructed using Internal Transcribed Spacer 2 (ITS2) ribosomal DNA. There is not ITS2 Sequence reference of An. balabacensis from GeneBank. Samples from endemic area, Purworejo, Central Java, Indonesia. Length of sequence ITS2 An. balabacensis are 343 anda 827 bp. GC content is variation between 58% until 65%.
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