22Replication initiation in eukaryotic cells occurs asynchronously throughout S phase, yielding early 23 and late replicating regions of the genome, a process known as replication timing (RT). RT changes 24 during development to ensure accurate genome duplication and maintain genome stability. To 25 understand the relative contributions that cell lineage, cell cycle, and replication initiation 26 regulators have on RT, we utilized the powerful developmental systems available in Drosophila 27 melanogaster. We generated and compared RT profiles from mitotic cells of different tissues and 28 from mitotic and endocycling cells of the same tissue. Our results demonstrate that cell lineage has 29 the largest effect on RT, whereas switching from a mitotic to an endoreplicative cell cycle has little 30 to no effect on RT. Additionally, we demonstrate that the RT differences we observed in all cases 31 are largely independent of transcriptional differences. We also employed a genetic approach in 32 these same cell types to understand the relative contribution the eukaryotic RT control factor, Rif1, 33 has on RT control. Our results demonstrate that Rif1 can function in a tissue-specific manner to 34 control RT. Importantly, the Protein Phosphatase 1 (PP1) binding motif of Rif1 is essential for 35 Rif1 to regulate RT. Together, our data support a model in which the RT program is primarily 36 driven by cell lineage and is further refined by Rif1/PP1 to ultimately generate tissue-specific RT 37 programs. 38