What drives gene evolution remains to be answered. We try to address this question by studying the gene evolution across closely related yeast genomes. The nucleotide substitution and indel rates have been quantified for all the genes with good data, from which genes with high or low evolutionary rates are identified. Detailed analyses using a systems biology approach reveal the relationship of evolutionary rates to the location and function of the coded proteins, the gene expression levels, the essentiality of the gene, as well as the network positions of the protein products in protein-protein interaction, and the structural characteristics of the coded protein. Such results may help address the general question on the drivers of gene evolution at genomic levels.