Nudibranchs, also known as sea slugs, represent a high species diversity within Heterobranchia (Mollusca, Gastropoda); however, the systematics within this order remain controversial. The mitochondrial genome has been widely used in the phylogenetic reconstruction of mollusks, but the corresponding data on Nudibranchia are limited, hindering understanding of the phylogenetic relationships of this group. In the present study, the complete mitochondrial genomes of 11 species belonging to 8 families and 10 genera were newly sequenced and compared with the 64 previously published mitogenomes for analysis. All newly sequenced mitogenomes were double-stranded circular molecules ranging from 14,299 to 14,880 bp. A total of 37 genes, including 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNA), and 22 transfer RNA (tRNA) genes, were encoded among all species. Of these 37 genes, 24 are encoded on the heavy strand and 13 on the light strand. The mitogenomes showed variations in AT content, GC skew, and AT skew. The gene orders of Nudibranchia indicated that gene transpositions and inversion had occurred within Hypselodoris. Based on the nucleotide sequences of 13 PCGs and 2 rRNA genes, the phylogenetic relationships of Nudibranchia have been reconstructed at family level. The phylogenetic analyses confirmed that Nudibranchia can be divided into Doridina and Cladobranchia with high support. However, the monophyly of Chromodoridoidea within Doridina is rejected due to the isolated positions of Actinocyclidae and Cadlinidae. Within Cladobranchia, the non-monophyly of Fionoidea was revealed since the fionoid group Coryphellidae clusters with Aeolidioidea. Molecular evidence, along with morphological characteristics, indicates that misidentifications of nudibranch species has been frequent in public databases. The present study suggests that the systematics within Nudibranchia needs further revision.