The tropical genus Cryptocarya is known for its valuable timber and the constituents in these trees show potential for medicinal properties. However, the phylogenetic relationships among species in Asia remain unclear. Here, we report the first mitochondrial genome for Cryptocarya kwangtungensis, consisting of 758,020 bp, including 43 protein-coding genes, 23 tRNA genes and three rRNA genes, with 234 simple sequence repeats, and 1275 dispersed repeats, 35 homologous DNA fragments between the mitogenome and the plastome. Comparative genomic analysis indicated frequent recombination events among the sequences of five magnoliids mitogenomes and only five conserved clustered genes. Further phylogenetic analyses based on 91 mitochondrial regions and nuclear ribosomal cistron sequences of 21 species compound three well-resolved congruent groups for the Cryptocarya species in Asia, both of which support the genus divide into three clades, suggesting that the mitogenome sequence can provide strongly supported relationships within the genus in the family Lauraceae.