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Cellular lineage histories and their molecular states encode fundamental principles of tissue development and homeostasis. Current lineage-recording mouse models have insufficient barcode diversity and single-cell lineage coverage for profiling tissues composed of millions of cells. Here, we developed DARLIN, an inducible Cas9 barcoding mouse line that utilizes terminal deoxynucleotidyl transferase (TdT) and 30 CRISPR target sites. DARLIN is inducible, generates massive lineage barcodes across tissues, and enables the detection of edited barcodes in ∼70% of profiled single cells. Using DARLIN, we examined fate bias within developing hematopoietic stem cells (HSCs) and revealed unique features of HSC migration. Additionally, we established a protocol for joint transcriptomic and epigenomic single-cell measurements with DARLIN and found that cellular clonal memory is associated with genome-wide DNA methylation rather than gene expression or chromatin accessibility. DARLIN will enable the high-resolution study of lineage relationships and their molecular signatures in diverse tissues and physiological contexts. [Display omitted] • DARLIN generates massive barcode diversity and labels ∼70% of profiled cells • DARLIN identifies early fate bias among HSCs and their transcriptomic signatures • DARLIN reveals low-level HSC circulation between bone-marrow niches in adulthood • Strong clonal memory in DNA methylation rather than mRNA or chromatin accessibility DARLIN is an inducible barcoding system that allows for lineage tracing and analysis across mouse tissues as well as combined transcriptional and epigenomic single-cell measurements. [ABSTRACT FROM AUTHOR]