<p>Marigolds (<i>Tagetes</i> spp.) are widely cultivated for ornamental, medicinal, and industrial purposes, yet efficient regeneration protocols, particularly for French marigold (<i>Tagetes patula</i> L.), remain limited, hindering genetic improvement efforts. This study reports the development of an optimized regeneration system for African (<i>Tagetes erecta</i> L.) and French marigolds through indirect organogenesis using cotyledon explants. Nine cultivars were evaluated for callus induction and shoot regeneration under varying auxin-to-cytokinin ratios using naphthaleneacetic acid (NAA) and benzylaminopurine (BAP). Genotype-specific responses were observed in both callus induction and shoot regeneration. Callus induction was most effective in ‘Bonanza Flame’ and ‘Marvel II Yellow’ at a 1:1 NAA:BAP ratio (1.0&#xa0;mg L⁻¹ each). Shoot regeneration reached up to 80% in orange-flowered French marigolds (‘Bonanza Deep Orange’, ‘Hot Pak Orange’, ‘Hot Pak Fire’) on 0.2&#xa0;mg L⁻¹ NAA + 4.0&#xa0;mg L⁻¹ BAP. Yellow-flowered genotypes exhibited excessive rooting, which was mitigated by increasing cytokinin concentrations; a 1:5 auxin-to-cytokinin ratio (0.5&#xa0;mg L⁻¹ NAA plus 2.5&#xa0;mg L⁻¹ BAP) effectively reduced root overgrowth while supporting shoot formation. This finding presents the first report of plant regeneration <i>via</i> indirect <i>de novo</i> organogenesis in French marigold, and the optimized protocol also significantly improves regeneration frequency in African marigold by fine-tuning hormone concentrations and addressing genotype-specific rooting responses. This study establishes an efficient, reproducible protocol for indirect organogenesis in French marigold and improves existing methods for African marigold, enabling future applications in genetic transformation and breeding.</p>