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YbB2 is hexagonal omega structure structured and crystallizes in the hexagonal P6/mmm space group. The structure is three-dimensional. Yb is bonded to twelve equivalent B atoms to form a mixture of face and edge-sharing YbB12 cuboctahedra. All Yb–B bond lengths are 2.73 Å. B is bonded in a 9-coordinate geometry to six equivalent Yb and three equivalent B atoms. All B–B bond lengths are 1.85 Å.
YbB6 is Calcium hexaboride structured and crystallizes in the cubic Pm-3m space group. The structure is three-dimensional. Yb is bonded in a 1-coordinate geometry to twenty-four equivalent B atoms. All Yb–B bond lengths are 3.04 Å. B is bonded in a 1-coordinate geometry to four equivalent Yb and five equivalent B atoms. There is one shorter (1.66 Å) and four longer (1.74 Å) B–B bond length.