Cannabis is an ancient multipurpose crop domesticated for fiber, seed, and pharmacologically active compounds. Optimization of these traits has involved independent selection on flowering time, sex expression, and inflorescence architecture, traits that ultimately determine yield and chemotype. Like other photoperiodic species, flowering in Cannabis is orchestrated by the circadian clock, which synchronizes diel gene expression with environmental light cycles. Using the Cannabis pangenome, multiple RNA sequencing (RNA-seq) time courses, and a genome-wide association study (GWAS) across a diverse panel of cultivars, we uncovered extensive structural variation in genes involved in photoperiod sensing, floral induction, and sex determination. Remarkably, unlike most angiosperms in which up to 50% of the transcriptome exhibits time-of-day (TOD) rhythmicity, only 9% of Cannabis transcripts cycle in leaf tissue and fewer than 2% in flowers. Core circadian regulators show haplotype-specific expression, and variation in key flowering genes provides potential markers for breeding and selection. We further dissect circadian and flowering time regulation in both male and female tissues, revealing distinct transcriptional programs linked to sex-specific developmental trajectories. Finally, by analyzing a population segregating for floral morphology, we explore the interplay between coding and non-coding variants shaping female flower form. Together, these findings establish a functional framework for integrating circadian and developmental genetics to optimize flowering and morphology in Cannabis, key levers for enhancing yield, cannabinoid production, and consistency under controlled cultivation.