Clustered grain rice (Cgr320) is a type of mutant material that clustered 2-3 grains on top of the main panicle. In order to clarify its genetic mechanism, we developed two F2 segregating populations derived from crosses between Cgr320 and WYJ24 or 93-11 and carried out the phenotypic observation experiment and analyses on genetic linkage of gene underlying Cgr320. The results showed that there were no significance differences in nine agronomical traits between Cgr320 and WYJ24 or 93-11 except clustered grain rice (Cgr), which showed recessive phenotype in F1 plants, indicating that the mutant is controlled by recessive gene. The segregation ration of mutant type plants to wild type plants in “WYJ24/Cgr320” F2 population was seriously deviated from the Mendel’s laws of 3:1, the chi-square (χ2) test values for Cgr genetic segregation were 7.71 and 144.87, respectively. Twelve SSR markers distributing on rice chromosome 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 and 12 were used to perform analysis on genetic linkage of gene underlying Cgr using 22 F2 recessive (mutant) plants, which showed serious segregation toward WYJ24, and the chi-square (χ2) test values for these markers were bigger than that of X2(0.05, 2) 5.991, this will mislead us to judge the correct linkage group of gene controlling Cgr. To our knowledge, this is a rare case of segregating distorting in rice gene mapping project analysis.