The objective of this paper is to assess increase and decrease of forest area and estimate shrub encroachment between 1997 and 2002 in open mire land using CIR aerial images, DSMs derived from it and LiDAR data. The present study was carried out in the framework of the Swiss Mire Protection Program, where changes of forested area are a key issue. The study area is located in the Pre-alpine zone of Central Switzerland. In a first step, high-quality DSMs were automatically generated from CIR aerial images of 1997 and 2002. This DSM generation is based on high accuracy, intelligent matching methods developed at ETHZ which are able to produce very dense and detailed DSMs that allow a good 3D modeling of both deciduous and coniferous trees and shrubs, and multi-temporal analysis of their growth pattern. In a second step, tree layers from both years were generated combining canopy height models derived from the DSMs and LiDAR DTM with a fuzzy classification of spectral information (NDVI) of CIR aerial images. In a third step, on the basis of these tree layers fractional tree/shrub covers were produced using explanatory variables derived from the DSMs in logistic regression models. Bias (due to different quality of input data) was estimated by analyzing the distribution of the fractional model differences. The corrected models reveal a general decrease of tree/shrub probability that indicates a decrease of forest and other wooded areas between 1997 and 2002. On the other side, the models also indicate real shrub encroachment and tree growth in open mire land. The study stresses the importance of high-resolution and high-quality DSMs and highlights the potential of fractional covers for ecological modeling.