Spikelets per panicle is one of the most important trait associated with rice yield component. In this study, IL28, 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, located in the interval RM3430 – RM20580. The fact that QTLs for panicle length and secondary branch number were mapped in the same interval as that for qspp6 indicated that this locus was associated with panicle structure. To map the QTL more precisely, substitution mapping of qspp6 using F4 lines was conducted. As a result, substitution mapping with ten F4 lines further narrowed the interval containing qspp6 to about 429kb between marker RM20521 and RM20562 based on the japonica 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 an applied breeding program.