The Cyanidiophyceae are a class of unicellular red algae that live in environments at the extremes of temperature, pH, salt, and heavy metal concentrations. These photosynthetic organisms have been able to occupy these rather unusual niches by acquiring a variety of genes from extremophilic prokaryotes and/or viruses via the process of horizontal gene transfer (HGT). Elucidating how the proteins encoded by these genes integrate into existing metabolic systems is crucial to understanding and evaluating the significance of HGT in eukaryotes and its role in conferring adaptive traits. This article addresses the fundamentals of HGT in model red algae, its function as a driver of evolution across the web of life with a focus on eukaryotes, and summarizes ongoing work and the future directions of this field.