Seed oils represent a major source of dietary lipid and an increasingly valuable feedstock for industrial applications. There have been several attempts to modify seed oil content and composition through biotechnological approaches, resulting in the identification of several 'bottlenecks' limiting the accumulation of unusual fatty acids in storage lipids of oilseed crops. It has been suggested that the substrate preferences of endogenous acyltransferases play an important role in the utilization of unusual fatty acids in transgenic oilseeds, and there is increasing evidence that mechanisms of 'acyl-editing' via phospholipids are also involved in substrate trafficking and utilization. In this review, we will examine acyltransferase substrate specificity and selectivity in the context of designing strategies to maximize the accumulation of unusual fatty acids using biotechnological approaches.