After wheat, rice is the second most important cereal grown in Iran that improvement of its economical characteristics always has important role in the rice breeding programs. In order to estimate the genetic parameters and identify salt-tolerant varieties and hybrids in seedling stage, seven female parents (Shah-pasand, Gharib, Tarom Mahalli, Ahlami Tarom, Hashemi and Dom Sepid) and four male parents (Khazar, Sepidroud, Dorfak and IR28) were crossed in a Line × tester mating design and their progenies were evaluated for traits related to salinity tolerance in Physiology Laboratory of Gonbad Kavous University. These traits include genetic code, chlorophyll content, root and shoot length, dry weight of root and shoot, sodium and potassium percentage in roots and shoots, ratio of sodium to potassium in roots and shoots and the percentage of seedlings’ stand. The results showed both additive and non-additive effects are involved in seedlings’ traits under salinity condition but non-additive effects play more important role in the genetic control of the traits. In this study, it was found that varieties of Hashemi (-0.101), Gharib (-0.284), Tarom Mahalli (-0.326), Sepidroud (-0.562) and Dorfak (-0.164) which possess good general combining ability are suitable for transferring more desirable genetic code and the higher percentage of seedlings stand and could be used in breeding programs to reduce the genetic code and increase the seedlings’ stand under salinity stress. In addition, investigation of specific combining ability for morphological and physiological characteristics showed that among the 28 crosses, three hybrids of Sepidroud×Ahlami Tarom, Dorfak×Hashemi and Dorfak×Sepidroud could be suitable for the breeding programs of salinity tolerance in seedling stage.