The coastal marten (Martes caurina humboldtensis) is a federally threatened small carnivore endemic to western Oregon and California. Due to their patchy distribution and elusive nature, coastal martens are challenging to monitor and most broad-based surveys use presence-nondetection methods such as camera-traps or scat detection dogs. Given limited information on population numbers, critical knowledge gaps for coastal marten conservation are population abundances, demographics, connectivity, and habitat associations. To fill these gaps, we generated genomic data and developed a SNP-based noninvasive genetic panel for sexing and identifying individual martens from scat samples. Our genomic data show genetic erosion of coastal martens consistent with small, isolated populations. We assess the effectiveness of our noninvasive panel for identifying individuals, tracking population structure, and estimating individual-level inbreeding and genetic diversity. Finally, we apply this panel to genotype marten scats collected between 2015-2023 and provide the first assessment of minimum population sizes and rangewide population structure. The ability to genotype scats opens the door to monitoring coastal marten density, demographics, and habitat associations. Future work will focus on developing a second noninvasive genetic panel targeted at building pedigrees and improving resolution for inference on genetic connectivity and developing similar panels for fishers (Pekania pennanti).