Budding and fission yeast continue to serve as outstanding models for biomedical research. However, while budding yeast is emerging as a model eukaryote for synthetic biology with many readily available fully-characterized toolkits, fission yeast has lagged partly due to the lack of similar resources. Furthermore, the development of genome foundries demands compatible platforms that enable modular, multi-part cloning with precision. Here, we present toolkits combining the Gateway and Golden Gate technologies for precise, automated, high-throughput cloning and genome engineering for both yeasts. For budding yeast, we modified a previously available toolkit into robotics-compatible vectors. For fission yeast, this platform provides a new set of vectors for modular assemblies, including a fully characterized collection of promoters and terminators. Additionally, we engineered a non-toxic, codon-optimized, genome-editing tool for efficient modifications of the fission yeast genome. Finally, we show the utility of the toolkit for precision cloning and the expression of heterologous human proteins in yeast.