This study introduces a method for rapid SNP discovery and genetic mapping using sequenced RAD markers. The approach involves generating RAD tags through restriction enzyme digestion and adapter ligation, followed by high-throughput sequencing. This method allows the identification of over 13,000 SNPs and the mapping of multiple traits in two model organisms, threespine stickleback and Neurospora crassa, using less than half the capacity of a single Illumina sequencing run. RAD tags are short DNA fragments adjacent to restriction enzyme recognition sites. By using different restriction enzymes, researchers can adjust the density of markers. The method also includes a barcoding system for sample multiplexing, which facilitates the identification of recombinant breakpoints in F2 individuals and the mapping of traits such as lateral plate armor loss and pelvic structure reduction. The study demonstrates the versatility of the RAD sequencing approach by identifying polymorphic markers and mapping an induced mutation in Neurospora crassa. The method allows for the efficient and cost-effective discovery of SNPs and genotyping of large populations. It also enables the identification of linked markers without the need for a reference genome, as shown by the identification of eighteen tags completely linked to the lateral plate phenotype. The approach is particularly useful for genetic mapping in organisms without a reference genome, as it allows for the identification of genomic regions associated with specific traits. The study also highlights the benefits of using Illumina sequencing over microarray-based RAD techniques, as it provides data on SNPs located outside the restriction enzyme recognition sites. The method is applicable to a wide range of organisms and offers significant advantages in terms of marker number, type, cost, and speed of analysis. It allows for the simultaneous discovery of novel SNP markers and genotyping of many individuals. The study demonstrates the feasibility of this platform by discovering over 13,000 polymorphic markers in two organisms and rapidly mapping three traits in two bulk segregant populations and 96 individuals. The approach is a powerful tool for genetic mapping and has the potential to be widely applied in various organisms.This study introduces a method for rapid SNP discovery and genetic mapping using sequenced RAD markers. The approach involves generating RAD tags through restriction enzyme digestion and adapter ligation, followed by high-throughput sequencing. This method allows the identification of over 13,000 SNPs and the mapping of multiple traits in two model organisms, threespine stickleback and Neurospora crassa, using less than half the capacity of a single Illumina sequencing run. RAD tags are short DNA fragments adjacent to restriction enzyme recognition sites. By using different restriction enzymes, researchers can adjust the density of markers. The method also includes a barcoding system for sample multiplexing, which facilitates the identification of recombinant breakpoints in F2 individuals and the mapping of traits such as lateral plate armor loss and pelvic structure reduction. The study demonstrates the versatility of the RAD sequencing approach by identifying polymorphic markers and mapping an induced mutation in Neurospora crassa. The method allows for the efficient and cost-effective discovery of SNPs and genotyping of large populations. It also enables the identification of linked markers without the need for a reference genome, as shown by the identification of eighteen tags completely linked to the lateral plate phenotype. The approach is particularly useful for genetic mapping in organisms without a reference genome, as it allows for the identification of genomic regions associated with specific traits. The study also highlights the benefits of using Illumina sequencing over microarray-based RAD techniques, as it provides data on SNPs located outside the restriction enzyme recognition sites. The method is applicable to a wide range of organisms and offers significant advantages in terms of marker number, type, cost, and speed of analysis. It allows for the simultaneous discovery of novel SNP markers and genotyping of many individuals. The study demonstrates the feasibility of this platform by discovering over 13,000 polymorphic markers in two organisms and rapidly mapping three traits in two bulk segregant populations and 96 individuals. The approach is a powerful tool for genetic mapping and has the potential to be widely applied in various organisms.