The location of pine marten records in northern Italy suggests that main rivers may play the role of natural corridors favouring this species’ colonisation of cultivated lowlands. We assessed the distribution and habitat use by the pine marten on a 35 km long stretch of the River Ticino. Surveys were carried out between October 2011 and June 2012 along linear transects in a 2 × 2 km grid. Using the variation in marking intensity as an indicator of habitat use, habitat selection was assessed at two landscape levels—at transect-scale by the χ 2 test with Bonferroni’s confidence intervals for the proportion of use, and at grid-scale by multiple linear regression. By a polymerase chain reaction–restriction fragment length polymorphism method, 91 faecal samples were assigned to the pine marten. Faeces were mainly located in wooded areas, while fields were avoided. At the grid-scale of analysis, marking intensity was positively related to the mean area of wooded patches and negatively to their mean perimeter-area ratio. This suggests that pine marten relative abundance may partially depend on the degree of fragmentation and structure of residual woods. The survey protocol allowed to assess the probability of detection. Occupancy models outlined that heterogeneity in detection probability may arise as a result of variation in marking intensity, i.e. the number of marking individuals. Our results suggest that the availability of both woodland corridors and wood patches are major factors shaping pine marten distribution in intensively cultivated plains and that non-invasive genetic surveys are a cost-effective method for future studies at a broader scale.