After growing in nutrient solution for 10 days, 84 rice varieties were harvested and measured in maximum root length (MRL) and root dry weight (RDW) separately. Twenty-seven of them were selected as representative variety for correlated fragments screening with amplified fragment length polymorphism (AFLP) technique. After surveying with 15 pairs of AFLP primers, 7 fragments from 4 pairs of primers were identified having significant correlation with MRL or/and RDW based on correlation coefficient analysis. One of them, "T3P3f", was cloned and sequenced, and its specific primers (Z336) were designed for the regular PCR amplication. Further analysis in 84 rice varieties revealed that correlation coefficient between Z336 and MRL was -0.193, much closer to the significant level of 5%; as between Z336 and RDW was -0.391, over the significant level of 1%. For the trait expression, Z336 could explain the root trait difference of 3.7% for MRL and 15.3% for RDW, respectively. The result shows the marker Z336 might tightly link with a QTL that has the negative relation with RDW expression. With a double haploid (DH) population from a cross of ZYQ8 and JX17, Z336 was finally anchored on rice chromosome 11 with a linked marker of 9.4 cM.