We have previously demonstrated that the complex [(L1O)MOOCl2], where L1OH = (2-hydroxy-3-tert-butyl-5-methyl phenyl)bis(3,5-dimethylpyrazolyl)methane, exists as both cis and trans isomers (Kail, B.; Nemykin, V. N.; Davie, S. R.; Carrano, C. J.; Hammes, B. S.; Basu, P. Inorg. Chem. 2002, 41, 1281-1291). Here, the cis isomer is defined as the geometry with the heteroatom in the equatorial position, and the trans isomer is designated as the geometry with the heteroatom positioned trans to the terminal oxo group. The trans isomer represents the thermodynamically more stable geometry as indicated by its spontaneous formation from the cis isomer. In this report, we show that for complexes of [(LO)MoOCl2], where LOH is the sterically less restrictive (2-hydroxyphenyl)-bis(3,5-dimethylpyrazolyl) methane, only the trans isomer could be isolated, while in the corresponding thiolate containing ligand (2-dimethylethanethiol)bis(3,5-dimethylpyrazolyl) methane (L3SH) only the cis isomer could be observed. In addition, we have isolated and structurally characterized the complex [(L1O)MoO(OPh)(Cl)], a rare example of a species possessing both cis and trans phenolates. Using DFT calculations, we have investigated the origins of the differences in stability between the cis and trans isomers in these complexes and suggest that they are related to the trans influence of the oxo-group. Crystal data for [(LO)MoOCl2] (1) include that it crystallizes in the triclinic space group P (1) over bar with cell dimensions a = 8.9607 (12) Angstrom, b = 10.596 (4) Angstrom, c = 13.2998 (13) Angstrom, alpha = 98.03 (2)degrees, beta = 103.21 (2)degrees, gamma = 110.05(2)degrees, and Z = 2. [(L1O)MoO(OPh)Cl].2CH(2)Cl(2) (2.2CH(2)Cl(2)) crystallizes in the triclinic space group P (1) over bar, with cell dimensions a = 12.2740 (5) Angstrom, b = 13.0403 (5) Angstrom, c = 13.6141 (6) Angstrom, alpha = 65.799 (2)degrees, beta = 64.487 (2)degrees, gamma = 65.750 (2)degrees, and Z = 2. [(L3S)Mo(O)Cl-2] (3) crystallizes in the orthorhombic space group Pna2(1), with cell dimensions a = 13.2213 (13) Angstrom, b = 8.817 (2) Angstrom, c = 15.649 (4) Angstrom, and Z = 4. The implications of these results on the function of mononuclear molybdoenzymes such as sulfite oxidase, and the DMSO reductase, are discussed.