High-quality mapping of genomic regions and genes between two organisms is an indispensable prerequisite for evolutionary analyses and comparative genomics. Existing approaches to this problem focus on either delineating orthologs or finding extended sequence regions of common evolutionary origin (syntenic blocks). We propose SyntenyMapper, a novel tool for refining predefined syntenic regions. SyntenyMapper creates a set of blocks with conserved gene order between two genomes and finds all minor rearrangements that occurred since the evolutionary split of the two species considered. We also present TrackMapper, a SyntenyMapper-based tool that allows users to directly compare genome features, such as histone modifications, between two organisms, and identify genes with highly conserved features. We demonstrate SyntenyMapper's advantages by conducting a large-scale analysis of micro-rearrangements within syntenic regions of 25 eukaryotic species. Unsurprisingly, the number and length of syntenic regions is correlated with evolutionary distance, while the number of micro-rearrangements depends only on the size of the harboring region. On the other hand, the size of rearranged regions remains relatively constant regardless of the evolutionary distance between the organisms, implying a length constraint in the rearrangement process. SyntenyMapper is a useful software tool for both large-scale and gene-centric genome comparisons.