Nonmarine stromatolites sporadically occur in the Lower Cretaceous Kanmon Group in northern Kyushu, Japan. We examined the mode of occurrence and morphological variations of the stromatolites that were found in the Wakino area, the stratotype of the Wakino Subgroup of the Kanmon Group, and analyzed their mineralogical compositions. These stromatolites occur at 7 horizons all from mudstone-dominant facies of the Barremian Lower Wakamiya Formation. The associated tepee structure, mud cracks, and gypsum pseudomorphs suggest that the stromatolites of the Lower Wakamiya Formation were deposited in extremely shallow-water environments with intermittent subaerial exposure. The studied stromatolites comprise 3 distinct morphotypes: flat, columnar, and nodular. XRD analysis confirms that all 3 types have the same mineralogical composition, i.e., calcite, quartz, and clay minerals. They are composed of alternating clastic layers and calcareous layers, or alternating siliciclastic carbonate layers and organic carbon-rich carbonate layers on a submillimeter scale. Based on their morphological characteristics, a sequential transition is suggested from the flat type to columnar type, then to nodular type. The columnar type has the greatest morphological variety, and shows a characteristic pattern of branching in which the bifurcation always initiates from an episodically intervened thick layer of siliciclastics. This suggests that the branching of stromatolite columns is likely triggered by blocking the upward growth of bacterial mats with intermittent supply of a thick sediment cover.