A highly publicized study in 2001 reported that maize landraces in Oaxaca, Mexico were found to contain transgenes, yet not all follow-up research has detected transgenes in the same region. Continued testing for transgenes in Mexican maize, and calls for the removal of transgenes from landraces, have only fueled the debate about the dynamics of gene flow from transgenic maize to landraces in Mexico. This paper reviews these recent findings and discusses how evolution may be expected to alter the frequency of transgenes in crop populations over time. Further, it shows that calls for removing transgenes must be interpreted in light of two ecological complexities: (a) it may be impossible to purge a particular gene from a population and (b) scientists' ability to accurately determine the presence or absence of transgenes is limited by challenges related to sampling. The paper concludes by outlining two ways forward for removing transgenes from landraces.