The emerging field of molecular ecology aims to improve the ecological predictability of transgenic crop plants. The most widely cultivated lines are Roundup-Ready® plants, which are genetically modified to be resistant to the broad-spectrum herbicide glyphosate. Recent publications demonstrate two ecological effects that were not anticipated: the widespread emergence of glyphosate-resistant weed biotypes and the formation of a metabolic herbicidal residue. Both effects appear to be due to the increased use of glyphosate rather than the genetic modification in the transgenic crop plant. With one prominent exception, opinions collected from the literature point towards a certain degree of resistance mismanagement and an inadequate testing of the ecological effects of extensive glyphosate use.