In a method of forming a conductive layer structure and a method of manufacturing a recess channel transistor, a first insulating layer and a first conductive layer are sequentially formed on a substrate having a first region a second region and the substrate is exposed in a recess-forming area in the first region. A recess is formed in the recess-forming-area by etching the exposed region of the substrate. A second insulating layer is conformally formed on a sidewall and a bottom of the recess. A second conductive layer pattern is formed on the second insulating layer to fill up a portion of the recess. A spacer is formed on the second conductive layer pattern and on the second insulating layer on the sidewall of the recess. A third conductive layer pattern is formed on the second conductive layer pattern and the spacer to fill up the recess.