Spikelets per panicle (SPP) is one of the most important traits associated with rice yield. In this study, IL28, a near isogenic line (NIL) developed by introgressing chromosomal segments from ‘Moroberekan’ into ‘Ilpumbyeo’ showed significantly higher number of spikelets per panicle than the recurrent parent, ‘Ilpumbyeo’. Quantitative trait locus (QTL) analysis in 243 F2 plants derived from a cross between IL28 and Ilpumbyeo indicated that a QTL for spikelets per panicle, qSPP6 was located in the interval RM3430 - RM20580. The Moroberekan allele increased SPP. The fact that QTLs for panicle length and the number of secondary branches were mapped in the same interval as qSPP6 appears to indicate that this locus was associated with panicle structure. To map the QTL more precisely, substitution mapping of qSPP6 using F3 lines was conducted. Substitution mapping with 41 F3 lines further narrowed the interval containing not only qSPP6 for spikelets per panicle but also qNDW6 for node width to about 680-kb between markers RM20521 and RM20572 based on Nipponbare genome sequence. The locus, qSPP6 is of particular interest because of its independence from undesirable height and flowering time. SSR markers tightly linked to the qSPP6 will facilitate cloning of the gene underlying this QTL as well as marker assisted selection for variation in SPP in the breeding program.