Hyorothermal conditions have been used in the preparation of a series of organic-inorganic hybrid materials of the cobalt-molybdophosphonate family. The reactions of MoO3, cobalt(II) acetate or cobalt(II) acetylacetonate, tetra-2-pyridylpyrazine (tpyprz), and organodiphosphonic acids H2O3P(CH2)(n)PO3H2 (n = 1-5 and 9) of varying tether lengths yielded compounds of the general type {Co-2(tpyprz)(H2O)(m)}(4+)/MoxOy{O3P(CH2)(n)PO3}(z). The recurring theme of the structural chemistry is the incorporation of {Mo5O15(O3PR)(2)}(4-) clusters as molecular building blocks observed in the structures of nine phases (compounds 2-9 and 11). The structural consequences of variations in reaction conditions are most apparent in the series with propylene diphosphonate, where four unique structures 4-7 are observed, including two distinct three-dimensional architectures for compounds 5 and 6 whose formulations differ only in the number of water molecules of crystallization. With pentyldiphosphonate, a second phase 10 is obtained which exhibits a unique cluster building block, the hexamolybdate [Mo6O18{O3P(CH2)(5)PO3)}(4-). In the case of methylenediphosphonic acid, a third structural motif, the trinuclear {(Mo3O8)(O3PCH2PO3)}(2-) subunit, is observed in compound 1. The structural chemistry of compounds 1-11 of this study is quite distinct from that of the {Ni-2-(tpyprz)(H-2 O)(m)}(4+)/MoxOy{O3P(CH2)(n)PO3}(z) family, as well as that of the copper-based family. The structural diversity of this general class of materials reflects the coordination preferences of the M(II) sites, the extent of aqua ligation to the M(II) sites, the participation of both phosphate oxygen atoms and molybdate oxo-groups in linking to the M(II) sites, and the variability in the number of attachment sites at the molybdophosphonate clusters. Since the charge densities at the peripheral oxygen atoms of the clusters are quite uniform, the attachment of {M-2(tpyprz)}(4+) subunits to the molybdophosphonates appears to be largely determined by steric, coulombic, and packing factors, as shown by extensive density functional theory calculations.