Freshwater fishes in California are challenged by anthropogenic activities, especially habitat fragmentation and the introduction of invasive species. Restriction Site-associated (RAD) Sequencing, a commonly applied Next Generation Sequencing technique in non-model organisms, can provide essential and actionable genomic information for managers to assess population statuses and for developing species conservation plans. In this dissertation, I explored the varied application of RAD sequencing to two native California species, Speckled Dace (Rhinichthys osculus) and Paiute cutthroat trout (Oncorhynchus clarkii seleniris). The Speckled Dace are widespread in western North America, and to this point, have been considered a single species. In Chapter One, the California Speckled dace is divided into three distinct evolutionary lineages based on the genetic differentiation detected by thousands of single nucleotide polymorphisms extracted using RAD sequencing. Paiute cutthroat trout are a subspecies of cutthroat trout threatened by competition and hybridization with introduced non-native trout. To protect and recover the subspecies, populations were previously translocated by conservation biologists to nine refuge populations thought to approximate historical habitats. Yet long-term genetic monitoring is required to monitor genetic diversity over space and time to assess the efficacy of these management actions. In Chapter Two, we selected 1,114 SNPs that generate comparable results in genetic diversity and genetic population structure to 6,187 SNPs in RAD sequencing after resolving technical questions related to the RAD sequencing approach. Results ultimately demonstrate the SNP panel is useful for genetic monitoring of population structure and heterozygosity, and thus helpful for conservation management. In Chapter Three, we applied 1,114 SNPs to estimate genetic diversity, and genetic population structure for all nine refuge populations. We also applied these SNPs to estimate parent-offspring relationships and the change of genetic diversity after the translocation between two refuge populations. We also applied these SNPs to estimate parent-offspring relationships and the change of genetic diversity after the translocation between two refuge populations.