Under natural conditions, plants are frequently exposed to transient or permanent soil waterlogging. Flooding of the soil with water with poor drainage drastically influences the soil physico-chemical properties, most notably soil oxidation-reduction potential, pH and O2 level. Thus, conditions of hypoxia or anoxia are commonly encountered by plant root systems. These O2 restrictive conditions dramatically have an effect on plant growth, development and survival. One in every of the simplest characterized plant responses to soil waterlogging is that the metabolic switch from aerobic respiration to anaerobic fermentation. In this study the effects of waterlogged were examined on seedling growth, metabolic, physiological and morphological responses of five species of timber trees (Casuarina cunninghamiana, C. glauca, Eucalyptus rostrata, Cupressus sempevirens and E. citrodora). The results indicated a wide variation among these timber tree species in their response to water logging. Casuarina cunninghamiana and C. glauca were more tolerant to waterlogging than the other species, followed by Eucalyptus rostrata then Cupres sussempevirens. E. citrodora was the least tolerant waterlogging species. Waterlogging treatment decreased the seedling growth and the leaf contents from carbohydrates, total and free phenols, chlorophylls and carotenoids as well as N, P and K contents in the leaves. On the other hand, waterlogging treatment increased both epinastic leaf angles, contents of total indoles, total free amino acids, chloride, sodium, calcium and magnesium in the leaves. Moreover, total free amino acids, total indoles, carbohydrates, total and free phenols contents were also increased in stems and roots of waterlogged seedlings.