The rice Rim2/Hipa is a stress-induced transposon superfamily recently identified in Oryza genomes. Genomic variation was found in the Rim2 core region among rice genetic resources/genomes, indicative of high genomic divergence accumulated during the Rim2 evolution. Based on the divergence and quiescent state of the Rim2 elements, a Rim2 paralog display-based fingerprinting approach was developed to effectively identify rice genetic resources and explore their genetic relationships within a set of rice germplasm including 45 accessions of O. sativa and 8 accessions of its wild relatives O. rufipogon. A dendrogram showed not only clear genetic diversity of rice germplasm, but also considerable genetic differentiation among wild rice resources. The wild rice relatives were either clustered as an independent group, or among the japonica varieties. This Rim2-based fingerprinting approach could also serve as a sensitive tool to identify rice hybrids from their parents, and variety stability, demonstrating its great potential in evolution study of rice genomes and in rice breeding and seed production.