Summary The evolutionary history of gymnosperms suggests that most species struggle in wet environments. However, baldcypress ( Taxodium distichum var. distichum ) thrives in wetlands, making it a prime candidate for studying flood tolerance in gymnosperms. Our study aimed to explore the genetic basis of this flood tolerance. We accomplished the first chromosome‐level genome assembly of baldcypress. Using Oryza sativa , Arabidopsis thaliana , baldcypress, and Taxus wallichiana , we compared gene expression, regulatory elements, and gene expansions between flood‐tolerant and flood‐intolerant plants. The baldcypress genome spans c. 7.82 Gb, containing 44 010 protein‐coding genes. We identified 409 commonly upregulated and 668 commonly downregulated orthogroups, representing conserved flood‐stress responses. Additionally, 352 orthogroups contained more upregulated genes in tolerant plants. Baldcypress appears to employ different evolutionary strategies than rice to withstand flooding. Both strategies involve the evolution of ERF‐VII transcriptional activation and antioxidant pathways. However, each species expanded distinct nodes within these pathways. Additionally, the evolution of spliceosome genes in baldcypress and energy‐producing genes in rice further reflects their differing evolutionary strategies. This study underscores the diversity and commonality of mechanisms underlying plant flood responses and tolerance, providing theoretical guidance for research on the genetic improvement of plant flooding tolerance.