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Rice is a major food crop in Sierra Leone with a high per capita consumption of 104 kg annually. Average yield (t/ha) is low, leading to a yield gap of 350,000 metric tons, which is met through import. A good number of rice farmers in Sierra Leone are cultivating on mangrove swamps, which are highly associated with salinity, resulting in the low average yield (tonnes per hectare). Salinity is a major abiotic stress devastating rice production in saline soils, including the mangrove ecology. Rice has been listed as the most salt sensitive cereal crop with a threshold of 3 dsm-1 beyond which yield begins to decline for most cultivated species. Understanding farmer’s knowledge on local rice varieties / land races and incorporation of molecular tools may enhance breeding for tolerance to salt stress in mangrove rice. The present study was undertaken to: (1) evaluate production constraints and varietal preferences of rice farmers in the mangrove ecology of Sierra Leone; (2) characterize the genetic diversity and population structure of mangrove rice landraces; (3) identify salinity tolerant QTL using DarT markers; and (4) estimate the relative efficiency of selection for tolerance to salinity in rice. A focus group discussion (FGD) and semi structured questionnaire were used in this study to sample responses from farmers. A total of 90 rice accessions collected from three districts (Kambia, Port Loko, and Moyamba) in Sierra Leone were evaluated in a completely randomised (CRD) design under screen house conditions in two replications. A cross between salt tolerance line (Nerica L9) and susceptible line (Sahel 317) was performed and a total of 462 F3:4 progenies were generated. The progenies, together with the two parents, were evaluated for tolerance to salinity in two replications under field conditions in Mbe, AfricaRice, Bouake. The 462 F3:4 progenies were genotyped for tolerance to Salinity using 13,432 SNP markers. Selection index and morphological characters were determined using BC1F3 populations. The present study identified major production constraints such as high cost of labour, salinity, lack of credit, lack of access to improved seeds and fertilizer, crab damage pest and diseases as most important. High yield, tall plant height, late maturity, good taste and high tillering ability were the top five traits farmers considered in selecting a variety. The cluster analysis found four distinct groups within the 90 germplasm which were also confirmed by the molecular analysis. The present study identified two major QTL (qDTF1.1 and qDTF1.2.) for time to 50% flowering on chromosome one, One major QTL (qDTF2) for the same trait on chromosome two. Two major QTL (qPH1.1 and qPH1.2) for plant height on chromosome one. Two QTL on chromosome 1 (qPN1) and chromosome two (qPN2). The study found that salt tolerance indices STI, DMP and TSI had discriminated among rice populations for yield under saline field conditions. Five agronomic traits including days to 50% flowering, plant height, number of tillers, number of panicle and filled-grain showed strong and positive correlations with grain weight hence are good selection indices under salt stress. The findings highlighted above could provide useful information for breeding for salt tolerance in mangrove rice in Sierra Leone.