Metacarcinus magister, the Dungeness crab, is a commercially important species on the Pacific Northwest coast as the most profitable fishery in Oregon and an important ecological player as both predator and prey. Understanding the spatial distribution of Dungeness throughout different life history stages is beneficial both ecologically and economically. Zostera japonica is an established invasive species of seagrass in the Pacific Northwest and may also be important habitat for recently settled juvenile Dungeness. We examined the distribution of juvenile Dungeness in May 2013 among Z. japonica, Z. marina, and open habitats in the Yaquina Bay Estuary in Newport, Oregon. We correlated Dungeness abundance with habitat, shoot density and biomass of seagrass, tidal height, and abundance of Hemigrapsus oregonensis, another local species of crab. Our results indicate that Dungeness preferred seagrass habitats to open mud, but had no apparent preference among different species of seagrasses, despite the correlation of Dungeness abundance with seagrass biomass. This study increases scientific understanding of the life cycle of Dungeness crabs and the importance of estuarine habitats, which must be protected in order to achieve a sustainable fishery.