Abstract: The mandarin fish has been recently becoming one of the most important aquaculture fish species in China be-cause of its good meat quality and protein composition1I mproving the production of these fish is a continuing goal of the aq-uaculture industry, and a better understanding of the molecular control of the muscle structure and development in this commercially important species could prove beneficial for more economic rearing and quality of production1Therefore,we intended to investigate what genes control the development of large amount of high-quality white muscle in this species, which may provide foundation for the understanding of itsmyogensis and information to refine musculature for aquaculture1 cDNA microarray is a powerful tool for the assaying of an organism’ s gemone and expression profiles1However, it is relatively behind in fish because limited arrays available1In order to obtain the gene expression profile and screen differ-entially expressed genes in muscle tissues in themandarin fish,we applied theAffymetrix zebrafish cDNA microarray heter-olously hybridized to both themadarin fish, Siniperca chuatsi and the silver carp, H1molitrix1Total RNAswere isolated from the muscle tissues of the two species of fish and labeled with biotin, and hybridized to Zebrafish cDNA gene chips1Hybridized microarray chips were scanned with Affymetrix 418 Array Scanner1All expression signals from the hy-bridization to 156.7 genes in zebrafish cDNA array were analyzed by R/Bioconductor software (http://www1bioconductor1org) 1Background correction and normalization were done by the methods of Robust multi-Array Aver-age known as gcRMA in R/Bioconductor1Out of 15617 genes in Zebrafish cDNA chips, total of 375 geneswere identified to be significantly expressed in themuscle tissuesof the two fishes1Compared to the silver carp, 180 genes are up-regulated and 195 are down-regulated in the madarine fish’ smuscle tissues1Among the 180 up-regulated genes, 49 genes are func-tionally known and 131 are unknown1The 49 known genes could be categorized into seven functional groups and several of them are considered aspotential candidates related to the fish’ smuscle structure and development1Several genes related to the muscle structure and meat textureswere identified, including myosin heavy chain gene (MYH),myofiber linker gene (plectin) and cytoskeletal structure genes (tubulin and actin) 1In themandarin fish,myosin heavy chain gene is expressed extremely higher at 3-% than that in the silver carp (Tab1-) and this large amount ofmyosin heavy chain protein expres-sion may reflect to the large abundance of high-qualitywhite muscle in this fish1Plactin identified from mammalian muscle tissue is another gene directly related to muscle structure and it functions as a cytolinker to cytoskeletal proteins and signal transductor1Plactin was expressed 16.5% higher in the mandarin fish than that in silver carp (log-ratio at 3195/3130). Titin gene was also highly expressed in both of the two fish1These results indicated that the muscle tissue of the mandarin fish was highly endurant and elastic1A cluster of genes functioning in cytoskeleton and dynamics including tubulin iso-forms, actin and microtubule-associated protein genes were quite abundantly expressed in the muscle of the mandarin fish1This group of genes played important roles in muscle cell structure, cell division and material transportation1In com-parison to the silver carp, both alpha-and beta-tubulin were expressed at 21% and 17% higher in themandarin fish,which suggested that high amount of tubulin protein in muscle cells of the mandarin fish may be directly related to itsmuscle e-lastic feature1 This is the first study using zebrafish cDNA microarray to heterogonous hybridization of other evolutionally far from fish species, and this information can be used to help select strains of high quality ofmuscular species for aquaculture industry and to provide a better understanding of gene expression profiles in relation to their biological functions in muscle tissue of different fish species.