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Herbaceous peony (Paeonia lactiflora Pall) is resistant to drought but not waterlogging. The main production areas of peony are prone to waterlogging, seriously affecting the growth and development of herbaceous peony. Polyamines have been observed to significantly enhance the ability of plants to defend and repair adverse damage and affect the synthesis and accumulation of the endogenous growth hormones indole-3-acetic acid (IAA) and abscisic acid (ABA). In this study, two herbaceous peony varieties ('Lihong', 'Qihualushuang') with different waterlogging tolerances were selected for artificial simulated waterlogging treatment to observe their morphological indexes and to determine their endogenous polyamine and hormone contents. Simultaneously, transcriptome sequencing and bioinformatics analysis were performed, focusing on screening differentially expressed genes in the polyamine metabolism pathway. The results showed that flood-tolerant varieties of herbaceous peony respond to waterlogging stress by continuously synthesizing spermidine (Spd) and spermine (Spm) through putrescine (Put) to counteract adversity. In the waterlogging-intolerant varieties, the expression of polyamine oxidase-related genes was annotated; their response to waterlogging stress was the simultaneous degradation of Spm and Spd to Put in the process of synthesis, and a decrease in the accumulation of Spm and Spd led to the early appearance of the symptoms of damage. In addition, polyamines influence key hormones that respond to plant adversity (IAA; ABA). The objective of this work was to initially analyze the mechanism of the polyamine signaling pathway in response to flooding in herbaceous peonies for further in-depth research on the mechanism of flooding tolerance in herbaceous peony, screen flood-tolerant varieties, and promote of their use. [ABSTRACT FROM AUTHOR]