Phenotype at crop level is the result of the interaction among many genes whose expression is often dependent on environmental conditions and developmental stage. Multilevel, computer-based, data integration thus plays a fundamental role in the understanding of many important agronomic traits such as yield and resource use efficiencies. Bioinformatics is the key for realizing the full potential of post-genomic revolution moving plant science toward crop systems biology. This manuscript will explore the benefit of bioinformatics application to plant research and, particularly, to crop science. Plant biologists and information technology specialists can contribute equally to such a task by organizing their work in a collaborative and interdisciplinary manner, thus applying in the most effective way their different technical skills to solve agricultural problems.