Rice (Oryzasativa L.) is an important crop that vital to the lives of billions of people providing almost 23percent of the calories intake. Most of the yield related traits are quantitative in nature. To improve these traits, quantitatively traits loci (QTL) are needed to be identified. Major QTLs have the tendency to be detected across populations and it mainly depends on high phenotypic variations for respective traits. Panicle characteristics are the main determinant of rice yield. Several investigations related to the identification of quantitative trait loci (QTLs) for these traits have been reported. Present studies were carried out to screen the QTLs in Malaysian rice cultivars for the selection of desirable plants through marker assisted breeding. Malaysian rice cultivars were evaluated for three panicle traits; panicle length, number of panicle per plant and number of grains per panicle. Eight microsatellite markers, which have shown association with panicle traits in the literature, were selected to identify the microsatellite loci for panicle traits. Among these microsatellites markers, RM310 distinguished the Malaysian rice varieties based on number of grains per panicle. It is therefore suggested to utilize microsatellite marker RM 310 in molecular screening of rice breeding populations to identify the plant possessing high numbers of grains.