Two separate tank-based trials have been conducted with adult female Scylla serrata to disclose the influence of salinity and temperature on their reproduction and moulting physiology. The first trial involved holding adult crabs for 28 days in four different salinity levels (S 15 ppt, S 25 ppt, a control S 35 ppt and S 40 ppt). The temperature trial tested four treatments (T 20 °C, T 25 °C, T 30 °C (control), and T 34 °C) for the same time period. Haemolymph ecdysone and Brix index were measured, and the relative expression level of genes related to reproduction (Vitellogenin receptor gene VtgR, Vitellogenin gene VtG, and sulfur oxidation enzyme gene SoxB2) and moulting (Ecdysone receptor gene EcR) were analysed following both trials. Additionally, the expression profile of HSP70 (heat shock protein) and Na+/K+-ATPase were analysed, as potential stress biomarkers for thermal and salinity shocks. The specific growth rate (SGR%), hepatopancreatic index (HPI), gonadosomatic index (GSI), and maturation stages at the end of trial have been compared. Major water quality parameters i.e., dissolved oxygen, pH, NH3, NO2 and NO3 were monitored and maintained stable for all treatment groups in both trials. The results of this study provide important information on factors influencing the reproductive physiology of mud crabs (Scylla spp.), which have high socio-economic value as a seafood product across the Indo-West Pacific.