A clear understanding of genetic diversity in weedy rice is important in improving protocols for its conservation, ex situ. To this end, Asian collections of weedy rice together with accessions of the wild AA genome species Oryza nivara Sharma et Shastry and Oryza rufipogon Griffith, and the cultivated species, Oryza sativa L. were characterized using 16 qualitative morphological traits and 18 SSR markers. The Shannon-Weaver index (H’) revealed higher diversity in the weedy (mean H’ = 0.76) and wild O. nivara (mean H’ = 0.79) and O. rufipogon samples (mean H’ = 0.69) compared to the cultivated samples (mean H’ = 0.44). The weedy forms showed high preference (> 90%) for high grain shattering and awn presence. Cluster analysis based on the 16 qualitative characters revealed three major clusters where weedy accessions grouped with (1) O. rufipogon samples (2) O. nivara, O. rufipogon and indica rice samples, and (3) indica, aus, and japonica and a few O. nivara and O. rufipogon rice samples. Cluster analysis based on SSR data concurred largely with morphological analysis. Genetic diversity indices (number of alleles, observed heterozygosity, expected heterozygosity) detected by SSR markers were comparable between the weedy (1.64, 0.11, 0.23) and O. rufipogon (1.53, 0.19, 0.23) samples. Analysis of molecular variance (AMOVA) among the weedy forms revealed that differentiation within accessions accounted for 79% of the total variation.