Abstract: The molecular evolutionary process is known to be variable, both within and between genomes. However, the scale at which this process varies, and the scale at which factors underlying rates and patterns of molecular evolution vary, remain unclear. Understanding the temporal and physical (i.e., with respect to physical location in the genome) scales over which the evolutionary process and its constituent forces change is critical for addressing evolutionary questions in an appropriate context. To investigate the temporal scale at which single nucleotide substitutional patterns vary, I applied a recently developed maximum likelihood model, capable of estimating lineage-specific rates of single nucleotide substitution, to coding and noncoding sequences in the six sequenced species of the melanogaster group. This analysis provides strong evidence in support of lineage-specific substitutional patterns, suggesting that the assumption of substitutional pattern stability over evolutionary time is flawed. To begin to address the question of physical scale, I focused on recombination rate. Using a classical genetics approach, I examined the fine-scale structure of recombination rate in a 1.2 Mb region of the D. melanogaster X chromosome. This analysis reveals significant heterogeneity in the recombinational landscape of this region, though the range of recombination rates in this region is modest. Together, these analyses suggest that the molecular evolutionary process in Drosophila is heterogeneous on both temporal and physical scales.