Koi fish have been developed as carp varieties in Japan throughout the past two hundred years via strict selective breeding. Despite their significant commercial value as ornamental fish, the decisive characteristics for the value of individuals are poorly defined and often left to the subjective assessment of different judges. In order to facilitate breeding and the uniformity of the characterization of valued traits, research on the genetic basis of these traits is being carried out. Some of the most significant traits include the coloration itself, colour patterns throughout the body, the characteristics of the scales, the coverage of the body with scales and the size of the fins. Due to the large number of different pigmented cells and the recent genome duplication event that koi are believed to be part of they also serve as excellent models for various research in the fields of genome evolution, embryology, gene expression regulation and pigmentation. This paper focuses on the overview of the structure of the koi carp genome, differential expression of genes such as Mc1r, Foxd3 and Scarb1 and their regulation by miRNA and lncRNA molecules, especially miR-206, which was found to differentially regulate the expression of the Mc1r gene. The known mechanisms of trait inheritance and the genes by which they are regulated, the negative impact of strict selection and the lethality of homozygotes for certain sought after traits are also discussed, as well as an overview of the development of various pigmented cells during embryogenesis and the associated biochemical pathways of pigmentation.