Black spruce (Picea mariana (Mill.) BSP) and tamarack (Larix laricina (Du Roi) K. Koch) are the predominant tree species in the boreal peatlands of Alberta, Canada, where low nutrient availability, low soil temperature and a high water table limit their growth. Effects of flooding for 28 days on morphological and physiological responses were investigated in greenhouse-grown black spruce and tamarack seedlings in a growth chamber. Flooding reduced root hydraulic conductance, net assimilation rate and stomatal conductance, and increased water-use efficiency (WUE) and needle electrolyte leakage in both species. Although flooded black spruce seedlings maintained higher net assimilation rates and stomatal conductance than flooded tamarack seedlings, flooded tamarack seedlings were able to maintain higher root hydraulic conductance than flooded black spruce seedlings. Needles of flooded black spruce developed tip necrosis and electrolyte leakage after 14 days of flooding, and these symptoms were subsequently more prominent than in needles of flooded tamarack seedlings. Flooded tamarack seedlings exhibited no visible injury symptoms and developed hypertrophied lenticels at their stem base. Application of exogenous ethylene resulted in a significant reduction in net assimilation, stomatal conductance and root respiration, whereas root hydraulic conductivity increased in both species. Thus, although flooded black spruce seedlings maintained a higher stomatal conductance and net assimilation rate than tamarack seedlings, black spruce did not cope with the deleterious effects of prolonged soil flooding and exogenous ethylene as well as tamarack.