AbstractChaetoceros is one of the most diverse genera of marine planktonic diatoms. Chaetoceros species are common and may become dominant in coastal ecosystems. Many Chaetoceros species can develop harmful algal blooms with negative effects on the aquaculture industry. In this study, we constructed full‐length mitochondrial genomes (mtDNAs) for 12 Chaetoceros species, including eight known species and four undescribed species. The sizes of these mtDNAs are generally similar, varying from 34,174 to 39,411 bp. Despite extensive synteny conservation, discrete regions showed high variations, and based on these regions, a specific primer chaetomt1 for Chaetoceros species was designed. The availability of mtDNAs from various Chaetoceros species is not only valuable as a super‐barcode for phylogenetic analysis but also important for functional and evolutionary analysis of diatoms.