Adaptation to similar environments can create new species and this process can occur repeatedly to result in parallel speciation. Although the genetic basis of this parallel speciation is poorly understood, it is assumed to occur by new pairs of species forming via divergence from a single shared ancestor. The genomic analysis based on genome-wide SNPs constructed by RAD-seq technique, we found that a parallel speciation in phytophagous ladybird beetle species involves distinct historical and genetic processes in different species pairs in Japan. In one geographic region a species pair was formed by divergence from a single common ancestor and specialization on different host plants. In contrast, in another locality a new species was formed by hybridization between two different closely related parental species. The results indicate that individual species can contain much genetic variation derived from distinct processes, and that hybridization between populations can generate new highly distinct species even in the early stages of ecological speciation. The collective results illustrate complex origins of different species with a potential role for hybridization in facilitating this process.