The starting point for interpretation of any single cell sequencing data is the annotation of cell clusters in a given dataset. Cell type annotation in single cell ATACseq data is challenging due to lack of specifically designed tools and use of unintuitive cis- and transregulatory elements in single cell ATAC-seq data. This Technical Note explores and demonstrates three different strategies that vary in the amount of bioinformatics expertise required for annotating cell types in single cell ATAC-seq data.