The nearly isogenic nature of the introgression lines (ILs) provides a relative advantage over other segregating populations in the rapid implementation of pyramiding approach through crosses and marker analysis. A set of 126 ILs carrying various introgressed segments from a presumed wild progenitor, Oryza rufipogon Griff. Acc. W1944 in the background of an elite Korea japonica cultivar (O. sativa L.), Hwayeongbyeo, was constructed using the marker assisted selection (MAS) technique combined with repeated backcrosses. The 126 ILs have different W1944 segments on each chromosome, with 100% coverage of wild segments on chromosome 1, while for chromosome 10, the coverage was only 33.3%. The mean number of homozygous and heterozygous donor segments were 3 (ranging from 0 to 7) and 4.7 (ranging from 1 to 14.5), respectively, and 31.6% of introgressed segments had sizes of less than 10.5 cM. A total of 41 quantitative trait loci (QTLs) and two loci associated with pericarp coloration were identified. The number of QTLs per trait ranged from 2 to 6. Phenotypic variance associated with each QTL varied from 9.1 to 52.2%, with an average of 17.1%. For 11 (26.8%) of the QTLs detected in this study, the O. rufipogon-derived alleles contributed the desired agronomic effect despite the overall inferior characteristics of the wild phenotype. Favorable alleles from the O. rufipogon accession were identified for panicle number, panicle length, days to heading, secondary branches, spikelets per panicle, and 1,000-grain weight.