Primordial germ cells (PGCs) are germinal stem cells, the precursors of gametes – eggs and sperm. In mammals, PGCs are reprogrammed from somatic cells early in development and are subjected to genome-wide erasure of epigenetic modifications, in particular, DNA methylation. This process ensures that non-genetic traits acquired in the lifetime of an organism are almost never inherited to the offspring. In non-mammalian organisms this process has not been studied quantitatively and some studies indirectly suggest absence of epigenetic reprogramming in the germline. Lack of epigenetic reprogramming in PGCs may support a currently unappreciated process of transgenerational inheritance. Using the model organism zebrafish (Danio rerio) expressing the transgene Tg(vasa:vasa-EGFP), a specific molecular marker of PGCs, we have isolated these germline cells using fluorescence-activated cell sorting (FACS). Measurement of DNA methylation status is being undertaken using a high-throughput bisulfite sequencing technique called post-bisulfite adaptor tagging (PBAT). Initial bootstrap sampling experiments have shown that relatively few sequencing reads are required in order to accurately estimate genome-wide methylation levels (10,000 reads, ±4.8%), greatly reducing sequencing costs. Our study aims to explore the epigenetic reprogramming dynamics in non-mammalian vertebrates and a potential mechanistic evidence for transgenerational inheritance.