To study allelic frequency and association analysis of microsatellite markers with some traits related to pre-harvest sprouting in rice, 34 local varieties/ improved rice cultivars were planted in research field of Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran, in 2013 cropping season. Traits related to pre-harvest sprouting were measured in the field and recorded. Also the banding pattern of 20 microsatellite markers was determined and their association was evaluated with these traits. Results analysis of variance showed that had significant differences for all traits at 1% of probability level that implies high genetic variation for traits related to pre-harvest sprouting. Results of allelic diversity revealed average number of effective alleles, Shannon’s index and polymorphic information content equal to 2.95, 1.14 and 0.59, respectively. Association analysis between microsatellite markers and traits showed the highest coefficient of determination with 47% explained by four markers RM282, RM220, RM447 and RM320 for grain shape. For pre-harvest sprouting (%) and pre-harvest sprouting (%) based on the number of filled grain, a common marker, RM525, explained 9% and 14%  of the variation observed for these two characteristics, respectively. Markers RM525, RM447 and RM124 commonly showed 31% and 28% association with two traits, frequency of sprouted seeds in the panicle and Alpha-amylase enzyme activity, respectively. Therefore, due to significant association of these markers, scanning of adjacent chromosomal regions can be useful for identifying allels controlling traits related to pre-harvest sprouting in rice.