A hog liver enzyme that catalyzes the reversible conversion of 3-acetylenic fatty acyl thioester to (+)-2,3-dienoyl fatty acyl thioester has been purified to homogeneity. The enzyme is not inhibited by the allenic product that it generates. The same homogenous enzyme catalyzes the conversions of 3-cis- or 3-trans-acyl Coenzyme A derivatives to 2-trans-acyl-CoA derivatives. Four forms of the isomerase differing in charge (pI = 6.57, 6.83, 7.01, and 7.27) have been separated by isoelectric focusing. Ultracentrifugation and sodium dodecyl sulfate-gel electrophoresis indicate that each of these enzyme forms is dimeric and composed of two 45,000-dalton subunits. With 3-acetylenic substrates, all enzyme forms exhibit broad specificity for chain length (C6 to C12) and for the thioester moiety (N-acetylcysteamine (NAC), pantetheine, or CoA). The 3-cis and 3-trans olefinic substrates are active only in the form of their coenzyme A derivatives; their NAC thioesters inhibit competitively. Mechanistic studies favor an isomerization pathway by way of carbanion intermediates. The acetylene-allene isomerase described here and the reported crotonase-catalyzed hydration of allenic thioesters (Branchini, B.R., Miesowicz, F.M., and Bloch, K. (1977) Bioorg. Chem. 6, 49-52) may be responsible for the degradation of naturally occurring acetylenic and allenic acids.