1. Relationships between animal populations and their habitats are well known and commonly acknowledged to be important by animal ecologists, conservation biologists and wildlife managers. Such relationships are most commonly viewed as static, such that habitat at time t is viewed as a determinant of animals present at that same time, t, or sometimes as a determinant of animal population or occurrence dynamics (e.g. between t and t+1).
2. Here, we motivate interest in simultaneous dynamics of both habitat and occupancy state (e.g. species presence or absence) and develop models to estimate parameters that describe the dynamics of such systems.
3. The models permit inference about transition probabilities for both habitat and focal species occupancy, such that habitat transitions may influence focal species transitions and vice versa.
4. Example analyses using data from salamanders in the eastern United States are presented for (i) the special case in which habitat is characterized as either suitable or unsuitable and (ii) the more general case in which different habitat states are expected to influence occupancy dynamics in a less extreme manner (occupancy is possible in the various habitat states).
5. We believe that the integrated inference methods presented here will be useful for a variety of ecological and conservation investigations and attain special relevance in the face of habitat dynamics driven by such factors as active management, land use changes and climate change.