Pyrococcus furiosus alcohol dehydrogenase D (AdhD) is a highly thermostable member of the well-characterized aldo-keto reductase (AKR) superfamily. Its preference for secondary alcohols and NAD+ combined with promiscuous activity towards simple sugars, primary alcohols, and aldehydes makes it an attractive protein engineering candidate for applications such as biofuel cells and the development of artificial metabolic pathways. We have examined the mode of cofactor binding in this enzyme and explored the nature of its preference for NAD(H) vs NADP(H). Site-directed mutagenesis of the cofactor binding pocket identified those residues important for determining cofactor specificity and identified mutants with improved activity. Changing a histidine residue involved in binding the adenine half of the cofactor back to the consensus arginine residue (in NADP(H) binding AKRs) resulted in an order of magnitude improvement in activity with NADP(H). Additionally, a lysine to glycine mutation in the cofactor binding pocket increased activity with both cofactors. Mutagenesis was also performed within the substrate binding pocket in an attempt to improve activity with sugars or primary alcohols. Substrate specificity in the AKR superfamily is tailored through modification of surface loops near the active site. Multiple sequence alignments and homology modeling indicate these loops are severely truncated in AdhD, and likely contribute to its thermostability and broad specificity. Typically these loops are necessary to differentiate between various steroids and other large substrates, and their reduced size should not significantly impact the affinity for smaller primary alcohols and monosaccharides. We report on the kinetic parameters for wild-type AdhD and mutants with improved activities with these substrates. The results of this work will be applied to the continued evolution of novel specificities for this enzyme.