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Background: Rice, being the principal food crop and major nutritional source for more than half of the global population, is also an important source of livelihood in many South and South-East Asian countries. Amidst diminishing natural resources and many biotic-abiotic stresses, increasing the yield of rice varieties remains a challenging task. Identification of novel and yield augmenting alleles from stable rice hybrids is crucial to facilitate their marker-assisted transfer into various genetic backgrounds. Results: Quantitative trait loci (QTL) mapping using a population of 125 doubled haploid (DH) lines developed from the cross IR58025A/KMR3R and 126 polymorphic SSR; EST-derived SSR markers led to the identification of 12 each of major-minor effect QTLs for yield related traits. Major effect QTLs were detected for traits namely days to fifty percent flowering, test (1,000) grain weight, plant height, panicle weight, panicle length, flag leaf width, flag leaf length, biomass and total grain yield/plant explaining the phenotypic variability in the range of 29.95%-56.75%. QTL hotspots were detected on chromosome 3 for the traits, panicle length and total grain yield/plant and on chromosome 6 for the traits, panicle length, flag leaf length and total grain yield/plant. Though many of these QTLs were noted to co-localize with the QTL regions reported in earlier studies, five novel and major effect QTLs for panicle length, biomass, flag leaf width, panicle weight, plant height and three novel minor effect QTLs for panicle weight and fertile grains per panicle, were identified in this study. Conclusions: Through this study, both major-minor effect novel QTLs for crucial yield related traits, viz., fertile grains per panicle, panicle length, panicle weight were identified. Further, the QTL hotspots identified on two different chromosomes for flag leaf length, panicle length and total grain yield/plant shall not only help in understanding the underlying genetic mechanisms of yield regulation but also would provide an insight into the genetic synchrony among the various yield related traits in contributing for yield heterosis. The identified QTL hotspots after their validation can be deployed in breeding programs targeted towards improvement of yield heterosis.