In aquaculture, hybridization is used to produce animals with favorable traits. In present study, first the embryonic development of Caspian brown trout at 9 ± 1 ? C and then the potential hybrid vigor in triploid hybrids between female rainbow trout ( Oncorhynchus mykiss ) and male Caspian brown trout ( Salmo trutta caspius ) of aspect of the the gastrointestinal tract ontogeny was assayed and compared to the parental species. Larvae samples were collected for histology and enzymatic assays (amylase, lipase and trypsin) from the triploid hybrids and its parents at 3 to 45 days’ post hatch (dph). To know more about hybrid fish biology and possible mechanisms involved in their mortality, RNA-seq as one of the emerging Next-generation sequencing methods was used to evaluate transcriptome of the diploid and triploid hybrid fish and the parental species (female rainbow trout and male Caspian brown trout) at 21 days post hatch. Then, the biological function of each group was evaluated with emphasis on the expression of genes unique to each group. Morphological analysis of landmark stages of embryonic development revealed that first cleavage occurred at 189 degree?h, a many?celled blastoderm formed at 62 degree?days (dd), a germ ring at 72 dd, the neural keel stage at 88 dd, the blastopore closed at 137 dd, the eye became pigmented at 188 dd and the larvae hatched at 373 dd. The results showed that the development of the gastrointestinal tract (Gl-tract) and digestive enzymes of the triploid hybrid was more like the rainbow trout. The well-developed Gl-tract was formed with age and the pyloric caeca and also the U-shaped stomach were clearly visible at 26, 35 and 40 dph in the rainbow trout, triploid hybrid and Caspian brown trout, respectively. An abrupt increase in trypsin activity at 31, 35 and 45 dph, was identified in the Caspian brown trout, rainbow trout and the triploid hybrid, respectively. The hybrid grew better and had a faster gastrointestinal tract development than the Caspian brown trout, but the rainbow trout performed best overall. Analysis of transcriptome of the diploid and the triploid hybrid fish (between female rainbow trout and male Caspian salmon) and the parental species showed differences in the biology of fish produced and the effect of triploidy on the hybrid fish biology. The Gene set enrichment analysis revealed the enrichment of the GO terms such as muscle organ, bone morphogenesis and some immune genes terms. Initial analysis of the transcriptome of the produced fish showed difference in the function and location of the genes expressed in each group. GO terms related to the bone and the muscle development and organs such as heart were enriched in the diploid and the triploid hybrids. The highest number of the enriched GO terms belonged to the triploid fish between the rainbow trout and the Caspian salmon and the least GOs belonged to the rainbow trout. In the rainbow trout, just male meiotic nuclear division GO term was enriched. In the Caspian brown trout, Cilium or flagellum-dependent cell motility GO term had the highest enrichment score. In general, the results obtained in this study can be used as a basis for future studies in the aquaculture sector.