The purpose of this review is to introduce recent advances in research, development and application of chromosome manipulation techniques in Japan. Triploids have been induced and utilized to improve growth. In most cases, triploids are produced as all-female populations by using spermatozoa of artificially sex-reversed males, so as to assure their complete sterility. In contrast, triploid males show better gonadal development and sometimes generate functional spermatozoa, which give rise to inviable aneuploids in most species. Although induced tetraploids can be useful for mass production of triploids by mating with normal diploids, tetraploid lines have only been produced in rainbow trout by a few institutes belonging to prefectural governments. In most cases, the techniques to inhibit the first cleavage often result in very low survival and mosaicism. In the loach (Cobitidae), polyploid lines such as hexaploids have been developed by using natural tetraploid individuals as an intermediate step. Cloned fish can be produced by the second cycle of gynogenesis in the eggs of completely homozygous diploids, which were produced by inhibiting first cleavage after induction of gynogenetic and androgenetic development. The second cycle of androgenesis, using spermatozoa of completely homozygous males, can also generate clonal lines. The most serious technical problem of cloning is the extremely low survival of homozygous gynogenetic and androgenetic diploids, probably due to the expression of deleterious recessive genes and side effect of treatments. However, cloned populations have been realized in commercially important ayu Plecoglossus altivelis, amago salmon Oncorhynchus masou ishikawae, coho salmon O. kisutch, hirame (Japanese flounder) Paralichthys olivaceus, fancy carp Cyprinus carpio, and red sea bream Pagrus major. In hirame, a practical method for mass production of clones was proposed and better performance has been reported in a heterozygous clone, produced by hybridization between two different homozygous clonal lines. Repeated meiotic (polar body) gynogenesis may be more practical than cloning from homozygous gynogens as a method to generate isogenic lines. In meiotic gynogenesis, the proximal region of chromosomes should be homozygous, whereas the distal region should be heterozygous due to high rates of gene–centromere recombination. Consequently, similar genotypes are predicted in the second and later generations of gynogenetic progeny. Their isogenic nature has been confirmed by minisatellite, microsatellite, and other DNA analyses. Gynogenesis, androgenesis and cloning can be used for elucidation of genetic sex determination. The involvement of environmental factors has been indicated from the sex ratios of chromosomally manipulated populations of several species. Finally, the regulation of chromosomally manipulated fish by the guidelines and the integration of such techniques with molecular genetics for further gene mapping and transgenics are discussed.