Studies to date on reproductive development and gametogenesis in zebrafish have been limited by the availability of methods to visualize the developing germline. These include transient labeling approaches, such as injection of DNA or RNA encoding germline-localizing markers, or transgenic approaches that leverage germline promoters that are activated only after gonad formation. Degradation of injected elements before germline-specific zygotic promoter activation leaves a period when the early germ cells cannot be reliably labeled and tracked. To bridge this gap, Germ traCre and Germbow were developed: two Cre-based transgenic lineage tracing systems which provide the earliest inducible and targeted long-term labeling of germ cell precursors -primordial germ cells (PGCs) - and their progeny. It was recently demonstrated that the Germ traCre and Germbow systems are effective for investigating PGC differentiation and the establishment of the pre-gametic germline. This cell fate transition is critical for the formation of a functional vertebrate gonad but has largely been inaccessible. Using these systems, we lineage-traced early PGC contributions to the gonad and found that PGCs give rise to a more diverse repertoire of germ cell progeny than anticipated. It was further demonstrated that individual PGC contributions affect ovarian reserve composition and lifelong reproductive potential. Together, these systems permit access to gametogenesis from the earliest germ cell differentiation events to gamete maturation, making them useful systems for germline lineage tracing that can be applied to any stage of reproductive life. This article presents comprehensive protocols for clonal lineage tracing of zebrafish PGCs and their progeny in the developmental day 16 (d16) juvenile zebrafish gonad, as well as multispectral labeling and analysis of ovarian reserve composition in adult females. This study demonstrates how to use the systems and provide methods for staining, dissection, and imaging of the juvenile zebrafish germline.