Almost four decades have passed since the new field of ecosystem simulation sprang into full force as an added tool for a sound research in an ever-advancing scientific front. The enormous advances and new discoveries that recently took place in the field of molecular biology and basic genetics added more effective tools, have strengthened and increased the efficiency of science outputs in various areas, particularly in basic biological sciences. Now, we are entering into a more promising stage in science, i.e. 'post-genomics', where both simulation modelling and molecular biology tools are integral parts of experimental research in agricultural sciences. I briefly review the history of simulation of crop/environment systems in the light of advances in molecular biology, and most importantly the essential role of experimental research in developing and constructing more meaningful and effective models and technologies. Such anticipated technologies are expected to lead into better management of natural resources in relation to crop communities in particular and plant ecosystems in general, that might enhance productivity faster. Emphasis is placed on developing new technologies to improve agricultural productivity under stressful environments and to ensure sustainable economic development. The latter is essential since available natural resources, particularly land and water, are increasingly limiting.