The consequences of habitat fragmentation include reduced habitat availability, increased isolation and patch extinction. This study investigates the occupancy patterns of Lontra felina, a little known and endangered marine otter, on naturally discontinuous habitat and the relationship between otter occupancy and rocky seashore patches, patch size and isolation and human influences. Marine otter occupancy was determined through direct sightings and the presence/absence of spraints, and measured by logistic regression and general linear models. The study was conducted in Chile between 28°S and 40°S, and consisted of eight study sites. Within these sites, a total of 23 rocky seashore patches, 2.3–63.8 km long, were surveyed from January 2005 to March 2006. The strongest predictors of marine otter occurrence were rocky seashore patches larger than 5 km long and <6 km apart. These networks should be no farther than 20 km from contiguous (without sandy beaches) rocky seashore patches over 15 km long.