S-Acylation is a major post-translational modification, catalysed by the zDHHC enzyme family. S-acylated proteins can be modified by different fatty acids; however, very little is known about how zDHHC enzymes contribute to acyl chain heterogeneity. Here, we employed fatty acid azide/alkyne labelling of mammalian cells, showing their transformation into acyl-CoAs and subsequent click chemistry-based detection, to demonstrate that zDHHC enzymes have marked differences in their fatty acid selectivity. This was apparent even for highly related enzymes such as zDHHC3 and zDHHC7, which displayed a marked difference in ability to use C18:0 acyl CoA as a substrate. Furthermore, we identified Isoleucine-182 in the third transmembrane domain of zDHHC3 as a key determinant limiting the use of longer chain acyl-CoAs by this enzyme. This is the first study to uncover differences in the fatty acid selectivity profiles of cellular zDHHC enzymes and to map molecular determinants governing this selectivit