We investigated introgression in a mixed weedy population of oilseed rape (Brassica napus) and its relative B. rapa using species-specific AFLP-markers. The population was situated in a field relayed from conventional to organic cultivation 11 years ago. One-hundred-and-two B. napus or B. rapa-like plants were collected in a 3 m2 plot. Of these, one was a first generation hybrid (F1) and nearly half (44 plants) were introgressed, having both B. napus and B. rapa specific markers. The remaining plants apparently corresponded to pure species, with 50 having only B. rapa- and seven having only B. napus-specific markers. We compared the number of markers in the plants from the weedy population with the numbers in controlled backcross generations (BC1 and BC2). The marker distribution in the weedy population resembled the distribution in the second backcross generation most closely. Together with the cultivation history of the field, this suggests that the introgression process in the weedy mixed population has been in progress for some time. This study is the first to show introgression between B. napus and B. rapa under natural conditions.