The congenic strain, an inbred strain containing a small genomic region from another strain, is a powerful tool to assess the phenotypic effect of polymorphisms and/or mutations in the substituted genomic region. Recent substantial progress in the genetic studies of complex traits increases the necessity of congenic strains and, therefore, a quick breeding system for congenic strains has become increasingly important in model organisms such as mouse and medaka. Traditionally, more than ten generations are necessary to produce a congenic strain. In contrast, a quick method has been reported previously for the mouse, in which the use of genetic markers reduces the required number of backcross generations to about a half that of the traditional method, so that it would take around six generations to obtain a congenic strain. Here, we present an even quicker congenic production system, which takes only about four generations. The system can produce medaka congenic strains having part of the HNI-II (an inbred medaka strain derived from the northern Japanese population, Oryzias sakaizumii) genome in the HdrR-II1 (another inbred strain from the southern Japanese population, O. latipes) background. In this system, the availability of frozen sperm and genotype data of the BC1 male population makes it possible to start marker-assisted congenic production after obtaining the BC2 population. Our evaluation revealed that the system could work well to increase the percentage of recipient genome as expected, so that a congenic strain may be obtained in about one year.