Salt toxicity is the major factor limiting crop productivity in saline soils. In this paper, association mapping method was used to detect the distribution of possible associated markers with salt tolerance in rice seedlings. 138 rice accessions of diverse origin were used to identify marker–trait associations with five salt-tolerant physiological traits such as ability of biomass accumulation balancing of osmotic potential, controlling of Na+ and K+ concentrations with favorable their ratio under three levels of NaCl salinities (0.9, 1.5 and 3.0 bar at 25 °C), and were genotyped with 249 SSR markers. Analysis of population structure revealed four subgroups in the population. Linkage disequilibrium (LD) patterns and distributions are of fundamental importance for genome-wide mapping associations. The mean r2 value for all intra-chromosomal loci pairs was 0.0591. LD between linked markers decreased with distance. Marker–trait associations were investigated using the unified mixed-model approach, considering both population structure (Q) and kinship (K). In total, 236 marker–trait associations were identified using 249 different SSR markers covering 12 chromosomes. The results suggest that association mapping in rice is a viable alternative to quantitative trait loci mapping, and detection of new marker–trait associations associated with salt tolerance will also provide important information for molecular-assisted breeding and functional analysis of rice salt tolerance.