Metasequoia glyptostroboides (Cupressaceae) is a rare deciduous conifer which grows successfully in both aquatic and terrestrial environments. This tree has a narrow natural distribution in central China but is cultivated worldwide. Using histochemical staining and microscopy (both brightfield and epifluorescent), we investigated whether the phenotypic anatomical and histochemical plasticity in the fine adventitious roots of M. glyptostroboides has promoted the adaptation of this plant to aquatic and terrestrial environments. The fine root development and cortex sloughing of M. glyptostroboides occurs later in aquatic habitats than in terrestrial habitats. Anatomical and histochemical analyses have revealed that the apoplastic barriers in the primary growth of the fine roots consist of the endodermis and exodermis with Casparian bands, suberin lamellae, and secondarily lignified cell walls. There were also lignified phi (Φ) thickenings in the cortex. In both aquatic and terrestrial roots, secondary growth was observed in the vascular cambium, which produced secondary xylem and phloem, as well as in the phellogen, which produced cork. As compared to terrestrial adventitious roots, aquatic adventitious roots had multiple lignified Φ thickenings throughout the cortex, larger air spaces, dilated parenchyma, and dense suberin and lignin depositions in the exodermis. Our results thus indicate that phenotypic plasticity in the anatomical features of the fine adventitious roots, including apoplastic barriers, air spaces, and lignified Φ thickenings, might support the adaptation of M. glyptostroboides to both aquatic and terrestrial environments.