Rice breeding of salinity tolerance based on a combination of phenotyping, genotyping and analyzing of genetic relationship was aiming to create the next generation with stable tolerance. In this study, 99 rice lines of the OMCS2000*4/Pokkali population in BC3F2 generation were screened in saline environments of 0, 6 and 12 dS m-1 at seedling stage. The tolerant lines were continuously tested the Saltol gene with 2 tightly markers, RM3412 and RM8094. The population was employed for the assessment of correlation, genetic variability, heritability and genetic advance for the related traits. Through phenotyping and genotyping, the population was tolerant to 6 dS m-1 for 4 weeks and 12 dS m-1 for 2 weeks, in which, 21/99 rice lines was highly tolerant and carried the Saltol gene. In this population, SES score and fresh biomass were the most significant traits and could explain over 70% of variability. SES scores were negatively correlated to almost all other traits, strongly to biomass, moderately to plant height, and lowly to root length. Analysis of variance revealed that sufficient genetic variation has been created for all traits. Relative magnitude of phenotypic coefficients of variation was higher than genotypic coefficients of variation for all the characters under study indicating environmental influence on the traits. High heritability coupled with high genetic advance was almost traits, exception of dry biomass. These indicated that direct selection can be effective for salinity tolerance improvement in the population under study.