Linepithema humile is one of the most damaging invasive species worldwide. Although chemical control strategies have proven effective for L. humile, the susceptibility of these invasive ants to the insecticide fipronil differs markedly among genetically different supercolonies. In Japan, five mitochondrial L. humile haplotypes were identified from eleven prefectural regions and cities as of 2010. In 2012, a new population was found in Okayama Prefecture. Here, we analyzed mitochondrial DNA from L. humile workers from the Okayama population to better understand the genetic structure of ants in Japan and develop effective control strategies. According to COI-COII and cytochrome b gene sequences, the L. humile Okayama population haplotype was consistent with the ‘Japanese main’ supercolony—the most invasive supercolony worldwide. Hence, we believe that the Okayama population (Japanese main supercolony) can be easily eradicated because of its early invasion stage, relatively limited distribution range and high sensitivity to fipronil.