We sequenced and assembled the complete mitochondrial genome of Abscondita cerata from Nankang, Taipei City, Taiwan. The complete mitogenome of A. cerata is 16,964 bp long, and contains 13 protein-coding, 22 tRNA, and two rDNA genes. Nucleotide compositions of the mitogenome of the A. cerata are A: 43.93%, T: 36.74%, C: 11.05%, and G: 8.28%. The AT and GC skewness of the mitogenome sequence are 0.0891 and −0.1434, showing the genome composition skewness toward adenine and cytosine. The clade including all Lampyridae species is well supported. The result indicates that Luciolinae is a monophyletic group but Lampyrinae is not a monophyletic group, as Lamprigera yunnana, which was originally classified into Lampyrinae, is sister to Luciolinae. The genus Lamprigera may share a unique phylogenetic position in Lampyridae. The genus Luciola is a polyphyletic group and the genus Abscondita is a monophyletic group. A. cerata is the sister species to A. chinensis in China. Mitogenomic data from this study will provide useful molecular markers for further studies on the population genetics, speciation, and conservation of endemic species A. cerata in Taiwan.
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