Very little is known about the ecological characteristics of Cobitis species living in Turkey though their taxonomic and systematic features are well -documented. This study aims to contribute to the knowledge of the ecology of this genus by describing the habitats of three of Cobitis species of Turkey: C, fahireae, C. puncticulata, C, levantina. Cobitis fahireae is very common in the Aegean Region (Western Anatolia) and some creeks of the Marmara Region (Northwestern Anatolia) of Turkey. Cabitis levantina is endemic to the Orontes basin (Southern Anatolia). Similarly, Cabitis puncticulata has a very limited distribution in Lake Manyas and its tributaries in Marmara Region. Knowledge of the habitats of these rare species is very important for assessing the threatening factors. These bottom-dwelling species are very sensitive to any disturbance of benthic structure of streams, which is easily altered by human activities such as sand quarries, streambed rehabilitation, and drainage of agricultural and waste disposal into streams. Habitats of these three species are discussed herein this study in terms of hydrometeorological, morphologic and hydrophysical and chemical conditions.