The concepts of evolution and natural selection remain as some of the most challenging topics to teach. The difficulty in teaching these topics arises from the fact that evolution is difficult to observe, and computer simulations do not always result in a clear understanding of evolutionary principles. Recently, the Avida-ED software has been developed to simulate evolution in a laboratory setting. Unlike other simulations, Avida-ED allows students to manipulate the environment, change the genetics of the virtual organisms, and track offspring in real time. We have demonstrated, by using pretest and posttest questionnaires, that students gained a deeper understanding of evolutionary concepts by using this software. In particular, students showed the greatest increase in their ability to explain evolutionary concepts in answers to open-ended questions. Our results show that Avida-ED could be a useful tool in helping students understand and combat preconceived notions about evolution.