Fluctuating asymmetry (FA), in contrast with other asymmetries, is the bilateral asymmetry that represents small, random developmental differences between right and left sides. After nearly a century of using traditional morphometrics in the estimation of FA, geometric morphometrics (GM) now provides new insights into the use of FA as a tool, especially for assessing environmental and developmental stress. Thus, it will be possible to assess adaptation to various environmental stressors as particular triggers for unavoidable selection pressures. In this review, we describe measures of FA that use geometric morphometrics, and we include a flow chart of the methodology. We also describe how this combination (GM + FA) has been tested in several agroecosystems. Nutritional stress, temperature, chemical pollution, and population density are known stressors experienced by populations in agroecosystems.