This research delineates the phenological growth stages of Alternanthera species, showcasing variations influenced by seasons and geographic locations. Our study tracked distinct life cycles in A. paronychioides across diverse seasons and in A. sessilis from different locations, revealing intriguing disparities in certain growth stages. Notably, the vegetative and reproductive phases, marked by BBCH code stages 0–1 and 5–9 respectively, exhibited distinct transitions in these species. Germination, leaf development, flowering, fruit development, and senescence stages unveiled stark differences across seasons in pot experiments. However, field experiments showcased uniformity in growth stages, except flowering, irrespective of varied geographical origins, emphasizing the influence of environmental factors, particularly temperature and moisture, over geographic distinctions. Further exploration into the polymorphism of polyamine (PA) metabolism genes uncovered intriguing associations with growth stages. The spermidine synthase (SPDS) gene demonstrated consistent polymorphism, implying its involvement throughout vegetative and reproductive phases. Meanwhile, arginine decarboxylase (ADC) and caffeic acid O-methyltransferase (COMT) genes displayed heightened polymorphism during reproductive stages, possibly indicating stress tolerance during these critical phases. The insights gleaned from this comprehensive analysis not only enhance our understanding of Alternanthera species' growth dynamics but also propose tailored herbicide strategies targeting specific growth stages based on PA metabolism. These findings offer sustainable avenues for weed management while providing valuable contributions to agricultural practices and environmental regulation.