In nature, Mangroves grow at estuarines and coastal intertidal area. They have adaptive mechanism of physiological, morphological and structural characters to the water-logging conditions induced by the tidal effects. The development of mangrove aerenchyma was proved to be highly related to their adaptability to inundation, and also considered as the major factor to evaluate the mangrove tolerance to inundation. The root aerenchyma developments were compared between natural and artificial habitats by porosity measurement and paraffin section for Avicennia marina (Am), Rhizophora stylosa (Rs), Bruguiera gymnorrhiza (Bg), Kandelia candel (Kc) and Aegiceras corniculatum (Ac), five dominant mangrove species in southern China. The leaf and stem aerenchyma of these five mangrove species were also studied by paraffin section. Results indicated that the measurements of two methods were statistically significantly correlative (P<005) for root aerenchyma. The most of aerenchyma resulted from the roots for these five mangrove trees. The roots aerenchyma accounted for more than 50% except that root aerenchyma of Am in tidal habitats was 48.16%, and Ac in non-tidal habitats was 43.81% of the sum (in root, stem, and leaf). The aerenchyma of Ac, Bg, Am, Kc, and Rs was (1498±3.34)%, (27.83±2.3)%, (29.64±3.17)%, (30.09±4.12)%, and (42.12±3.14)% in natural intertidal habitats, respectively. This distribution of aerenchyma was accordant to the mangrove tidal zonation and vegetation successional sequence in the southern China coast. The root aerenchyma of Rs, Bg, Kc, Am, and Ac increased in non-tidal artificial habitats compared to natural tidal habitats, indicating adaptability to non-tidal conditions flooding for these mangrove species in some degree. The increase of root arenchyma development was least in Ac, while most in Rs. It was inferred that those species of less adaptive to inundation, i.e. Bg and Rs, increased their root arenchyma more to tolerate steady water level condition. They could be considered as more sensitive to water level change. By contrast, the species of more adaptive to inundation, i.e. Ac and Am, increased their root arenchyma less. This could be considered as a less sensitive phenomenon to water level change. Under non-tidal conditions, the aerenchyma of Ac, Am，Kc, Bg and Rs was (56.38±2.41)%, (40.88±1.03)%, (39.18±1.21)%, (35.70±0.57)% and (19.28±0.63)%, respectively. Judging from root aerenchyma developments in non-tidal habitats, their adaptabilities to the steady inundation condition were as following sequence: Ac > Am > Kc > Bg > Rs. The adaptability of mangrove to non-tidal inundation condition increased the feasibility.The result was important to enhance the survival rate of mangrove planting, and expand planting area for improving coast ecological services.