Weedy rice is a serious problem in Uruguayan rice fields since intensification of rice production started about 10 years ago. The genetic diversity of 26 weedy accessions of weedy rice and 6 Uruguayan cultivars were analyzed using AFLP (amplified fragment length polymorphisms) methodology. Abundant polymorphisms were found among samples tested. Using different methods of analysis three groups of samples were revealed. A relationship was found between three groups and morphological traits. One group had a black hull, purple apex and long awn (wild type traits) while another group had straw hull and apex, and short or no awn (domestication traits). The third group included the cultivars analyzed and some weedy rice samples. The weedy rice in this third group is presumed to most closely mimic cultivated rice and may have recently evolved. The results suggest that weedy rice adapts either to the natural environment or to cultivation. The former type with black hull and long awn may be easy to control because it can easily be seen. The later group may be difficult to control, particularly since the weedy rices within the cluster consisting of cultivars suggest that weedy rices are continually evolving in Uruguayan rice fields. The AFLP technique is very effective for assessing genetic diversity within weedy rice and will be very useful for fingerprinting of local cultivars of rice.