The first generation was MINAMOTO no Yoriyuki (a younger brother of MINAMOTO no Yorimasa), who was descended from Settsu Genji (Minamoto clan), and in the Kamakura period his grandchild MINAMOTO no Yoritsura became the jito (land steward) of Oguniho in Echigo Province (the present-day Oguni-cho, Nagaoka City, Nigata Prefecture) and took the name of Oguni.
摂津源氏の流れを汲む源頼行（源頼政の弟）を祖とする一族であり、頼行の孫である源頼連が鎌倉時代に越後国小国保（新潟県長岡市小国町）の地頭となり小国氏を称した。