Marker Assisted Selection method (MAS) has been used for precise introgression of new gen/QTLs (Quantitative trait loci) and development ofricevarieties with new traits. Usually this method take 6-8 crop seasons to achieve result and lead to creation totally new varieties. In current study, we are using newly developed method for introgression of new gen(s)/QTLs into elite crop variety - marker-assisted backcrossing (MABC). This method allowsrapid and precise transfer tolerance gen(s)/loci into high-yielding, but stress-sensitive varieties within shorter time.Marker assisted backcrossing may differ from other marker assisted breedingschemes because additional markers may be used for purposes other than target locus selection, in order to minimize linkage drag and accelerate the recovery of the recurrent parent through three levels of selection .i) foreground selection, ii) recombinant selection and iii) background selection. Three backcrosses were conducted to transfer positive alleles of saltol (salinity tolerance) and Sub1(Submergence tolerance) into popular rice varieties. All selected lines carry saltol or Sub1similar to the donor parent in genotyping and phenotyping studies, where they can grow normally in area with saline level up to 0.7% and stand submergence up to 15 days. At the same time their agronomic performances were the same as the original recipient variety. Background selection shows presence of nearly 100% genome of recipient lines. Field study shows that improved lines have the same characteristic of recipients, such as plant height, vegetation time, structure of plant, yield and grain quality…This study demonstrates potential for application of MABC for development of multiple tolerant rice varieties with increased tolerance to many stress factorsin the same varieties that are very important for adaptation to climate change – the main challengers for food production in 21 century.