Trait-specific characterization of rice landraces has significant potential for germplasm management, varietal identification and mining of novel gene/allele for various traits. In the current study, we have characterized 98 unique rice landraces collected from coastal regions of India, affected by submergence and salinity, based on Sub1 and Saltol quantitative trait loci (QTL) linked microsatellite markers. Among these genotypes, four genotypes (IC536558, IC536559, IC536604 and IC536604-1) collected from Kerala and two genotypes (AC34902 and IC324589) collected from West Bengal were identified with tolerance to submergence and salinity stress. A high level of genetic diversity of He = 0.349 and 0.529 at Sub1 and Saltol QTL region was detected by QTL-linked microsatellite markers, respectively. At Sub1 region one genotype, AC34902, was detected with maximum allelic similarity with FR13A, a known submergence tolerant variety. Besides, five genotypes (IC211188-1, IC536604-1, IC536604, IC536558 and IC536559) showed comparatively close genetic relationship with the salt tolerant variety FL478 for Saltol QTL and were clustered together in the neighbour joining dendrogram. Considering the haplotype structure, five genotypes (IC203801, IC203778, IC324584, IC413608 and IC413638) were identified which did not contain any common allele similar to FR13A but were still tolerant to submergence. These individuals need further characterization for identification of new alleles responsible for their tolerance.