Nowadays, Litopenaeus vannamei are the most important species of farmed penaeidae shrimp in the world that is rapidly replacing native species in areas aquaculture. Due to demand increase for this species culture, shrimp displacement to different areas may be associated with some potential pathogens transferred to new areas farmed. Therefore, in this study were prepared bi-osecurity conditions for specific disease-free production of L. vannamei. Thereafter, three populations (Molokaei, High health and mix of Molokaei and High health) of the shrimp various reserves were detected base on origin and genetic indexes such as: observed heterozygosity, expected heterozygosity, allele frequency, coefficient inbreeding, genetic differentiation, genetic distance and genetic identity. On the other hand, epidemiological studies indicate non pathogens (viral, bacterial, fungal and parasitic) recognition of different populations selected in the quarantine salon. The bioassay results showed that the average weight and length of the populations of High health and Mix significantly greater than was a population of Molokaei. The shrimp populations were stocked in fiberglass tank (five ton) and were kept separated in the quarantine salon. During maintenance shrimp of populations in the quarantine salon were evaluated living and non-living pathogens with PCR, microbiology and biochemical methods. There is not any pathogens detection from shrimp populations stocking in the quarantine salon, so the shrimps were carried over to pond for broodstock culture of specific pathogenic free
