Physicochemical properties and vertical distribution patterns of clay minerals were studied in the permafrost-affected soils from the tundra and sub-tundra larch open woodland of Tit-Ary Island. This unique complex is located in the Lena River Delta, Republic of Sakha (Yakutia). Despite the small size of the island and the fact that permafrost is close to the surface, several variants of pedogenesis determine the soil diversity in this area. The soils are characterized by various degrees of gleyic and stagnic properties due to sandy or loamy texture and location in the landscapes (top of the hills and steep or gentle slope). Mineral associations in the studied profiles are similar and are characterized by the predominance of two components: chlorite and illite. Iron hydroxide—lepidocrocite—occurs at the boundary of permanently frozen ground in the profile with pronounced spodic features. Smectitic clay identified in both horizons of this permafrost affected soil, as well as lepidocrocite, can be attributed to the result of modern pedogenesis.