Lineage tracing – tracking the relationships between cells through developmental time – has traditionally relied on the use of traceable dyes or genetically encoded markers to mark clones of cells. An alternative approach uses sequencing to identify mutations that accumulate in cells as they divide – and hence infer the relationships between cells by the presence of common mutations. Arrays of engineered CRISPR targets (barcodes) inserted into the genome, and injection of the cognate sgRNAs and Cas9, can generate mutations in a small genomic region, facilitating efficient analysis. However, this approach requires the generation of a transgenic cell or organism. James Sharpe and colleagues now develop a computational pipeline to identify endogenous CRISPR arrays that can be used as barcodes for lineage tracing. They apply this method in both zebrafish and mouse embryos, demonstrating that endogenous loci with multiple CRISPR target sites can be efficiently edited, and that lineage maps can be generated. Given the large number of potential CRISPR arrays in the genome, the approach could in principle be scaled up to allow whole-organism lineage tracing. This work adds to the growing battery of methods for high-throughput lineaging, and opens the door for CRISPR-based lineage analysis to be used in organisms for which transgenesis is difficult or impossible.