The greatest distributed mangrove plants in China, Kandelia obovate were affected by waterlogging stress for a long time, which seriously restricts its growth and development. We combined growth index observation, microscopic observation, RNA-seq, and WGCNA analysis to preliminically clarify the molecular mechanism of Kandelia obovata under waterlogging stress. RNA-seq high-throughput sequencing successfully identified 228 flooding stress response factors. WGCNA coexpression network analysis combined gene expression level and plant growth trait level to obtain 16 core genes related to waterlogging stress induction. Our study provides a new clue and useful gene resources for genetic improvement of forest resistance using molecular breeding techniques.