Speciation” was largely “speculation” two decades ago, at least with respect to a detailed and comprehensive mechanistic understanding of the origin of new species. Despite elegant classical work examining the genetic basis of interspecific differences and reproductive isolation and complementary studies of the ecological factors that can contribute to species divergence, speciation researchers lacked the tools to dissect the specific forces, traits, and genes involved. Thanks to the recent advances in molecular biology and genomic sequencing, detailed study of speciation is becoming feasible in many animal and plant groups. In fact, a dozen of “speciation genes” responsible for reproductive isolation between sibling species have been identified at the molecular level. Further, genetic changes leading to morphological differentiation among related species have been elucidated, supported by phylogenetic analyses at high resolution. We invited investigators to contribute both original research and review articles that would stimulate the continuing efforts to understand speciation and species differentiation from all perspectives, not only the genetic mechanisms but also the ecological and evolutionary causes.