Asian palm civet (
Paradoxurus hermaphroditus
) is one of the smallest palm civet which is least studied. Here, we report the first complete mitochondrial (mt) genome of Asian palm civet (
P. hermaphroditus
). The circular mt genome with a length of 16,706 bp contained 1 control region, 2 rRNAs, 13 protein-coding genes, and 22 tRNAs. Overall base composition of the complete mt DNA was 33.7% A, 30.5% T, 22.9% C, and 12.9% G. All the genes in mt genome of Asian palm civet (
P. hermaphroditus
) were distributed on the H-strand, except
ND6
and eight tRNA genes encoded on the L-strand. Maximum likelihood (ML) and Bayesian inference (BI) methods were used to infer the phylogenetic relationship of
P. hermaphroditus
. The phylogenetic analysis shows that all species from the family Viverridae cluster together, in which
P. hermaphroditus
exhibits the closest relationship with
P. larvata
.