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Conserved Ortholog Set II (COSII) markers represent a well-established resource for comparative genomics and phylogenetic analyses in the Solanaceae family. In this study, we conducted a comprehensive in silico assessment of COSII orthologs in Solanum lycopersicum L., Solanum tuberosum L., and Capsicum annuum L. using an integrated workflow that combined OrthoFinder-based orthogroup inference, hierarchical orthogroup (HOG) reconstruction, synteny mapping, and evaluation of copy number. We identified 2,853 COSII-associated orthogroups, of which 2,359 (82.7%) were shared among all the three species, forming a deeply conserved solanaceous core. Among the three species, 1,839 orthogroups represented strict single-copy loci, reflecting their high evolutionary stability. Across these loci tomato and potato retained nearly complete single-copy status, whereas C. annuum L. displayed moderate copy-number variation (mean 1.35 genes per orthogroup; 22% multicopy), with duplicated clusters enriched on chromosomes 1-3, as well as on unplaced scaffolds (CA00). Hierarchical orthogroup analysis revealed substantial gene family expansion at the ancestral Solanaceae node, followed by lineage-specific diversification within Solanum and Capsicum. Synteny mapping showed extensive collinearity among genomes, combined with localized breaks and rearrangements in pepper. Together, these findings highlight a dual evolutionary pattern in Solanaceae: a highly conserved COSII genomic backbone, alongside lineage-specific structural innovations in C. annuum. COSII remains a reliable marker system for phylogenetics, comparative genomics, and marker-assisted breeding. The observed Capsicum-specific multicopy expansions overlap genomic regions enriched for stress-response gene families, suggesting links between structural variation and abiotic stress adaptation.