The draft sequences for a number of completely sequenced genomes (both prokaryotes and eukaryotes) are now available in the public domain. This allows the comparison of these genomes using parameters such as genome size, gene number, chromosomes (size and length), gene structures (single exon and multiple exon), junk (noncoding intergenic region) DNA, introns, and exons along with their content and arrangement. An understanding of genome content in different species organisms has to be established in the context of molecular evolution through genome comparison. The study and comparison of genomes to establish evolutionary relationship is computationally exhaustive and mathematically challenging. This chapter highlights some of the issues associated with the study of eukaryotic genes, genomes, function, design, and evolution. It should be noted that our current understanding of genomes in perspective of their known size to current design, organism level function, and evolution is limited.