This comprehensive study examines the functional and evolutionary patterns of 5,873 clusters of predicted orthologs (KOGs) from seven eukaryotic genomes: *Caenorhabditis elegans*, *Drosophila melanogaster*, *Homo sapiens*, *Arabidopsis thaliana*, *Saccharomyces cerevisiae*, *Schizosaccharomyces pombe*, and *Encephalitozoon cuniculi*. The analysis reveals a conserved core of essential eukaryotic genes and significant diversification and innovation in eukaryotic genomes. Approximately 40% of KOGs, enriched in housekeeping functions like translation and RNA processing, are essential for survival and might approximate the minimal set of essential eukaryotic genes. The study also identifies 131 single-member, pan-eukaryotic KOGs, many of which have been uncharacterized but are likely essential. These proteins are often subunits of known or predicted multiprotein complexes, supporting the balance hypothesis of gene copy number evolution. Other KOGs show varied phyletic patterns, indicating lineage-specific gene loss and the 'invention' of new genes. Parsimonious scenarios of eukaryotic genome evolution and ancestral gene sets are reconstructed, revealing a core set of 3,413 genes for the last common ancestor of the crown group. The study highlights the importance of orthologous groups in understanding eukaryotic evolution and provides a basis for detailed reconstruction of ancestral eukaryotic forms.This comprehensive study examines the functional and evolutionary patterns of 5,873 clusters of predicted orthologs (KOGs) from seven eukaryotic genomes: *Caenorhabditis elegans*, *Drosophila melanogaster*, *Homo sapiens*, *Arabidopsis thaliana*, *Saccharomyces cerevisiae*, *Schizosaccharomyces pombe*, and *Encephalitozoon cuniculi*. The analysis reveals a conserved core of essential eukaryotic genes and significant diversification and innovation in eukaryotic genomes. Approximately 40% of KOGs, enriched in housekeeping functions like translation and RNA processing, are essential for survival and might approximate the minimal set of essential eukaryotic genes. The study also identifies 131 single-member, pan-eukaryotic KOGs, many of which have been uncharacterized but are likely essential. These proteins are often subunits of known or predicted multiprotein complexes, supporting the balance hypothesis of gene copy number evolution. Other KOGs show varied phyletic patterns, indicating lineage-specific gene loss and the 'invention' of new genes. Parsimonious scenarios of eukaryotic genome evolution and ancestral gene sets are reconstructed, revealing a core set of 3,413 genes for the last common ancestor of the crown group. The study highlights the importance of orthologous groups in understanding eukaryotic evolution and provides a basis for detailed reconstruction of ancestral eukaryotic forms.