Digital tracking technologies have considerably increased the amount and quality of animal trajectories, enabling the study of habitat use and habitat selection at a fine spatial and temporal scale. However, current approaches do not yet explicitly account for a key aspect of habitat use, namely the sequential variation in the use of different habitat features. To overcome this limitation, we propose a tree-based approach that makes use of sequence analysis methods, derived from molecular biology, to explore and identify ecologically relevant sequential patterns in habitat use by animals. We applied this approach to ecological data consisting of simulated and real trajectories from a roe deer population (Capreolus capreolus), expressed as ordered sequences of habitat use. We show that our approach effectively captured spatio-temporal patterns of sequential habitat use by roe deer. In our case study, individual sequences were clustered according to the sequential use of the elevation gradient (first order) and of open/closed habitats (second order). We provided evidence for several behavioural processes, such as migration and daily alternating habitat use. Some unexpected patterns, such as homogeneous sequences of use of open habitat, could also be identified. Our findings advocate the importance of dealing with the sequential nature of movement data. Approaches based on sequence analysis methods are particularly useful and effective since they allow exploring temporal patterns of habitat use in a synthetic and visually captive manner. The proposed approach represents a useful and effective way to classify individual movement behaviour across populations and species. Ultimately, this method can be applied to explore the temporal scale of ecological processes based on movement.