Knowledge of forest structures—and of dead wood in particular—is fundamental to understanding, managing, and preserving the biodiversity of our forests. Lidar is a valuable technology for the area-wide mapping of trees in 3D because of its capability to penetrate vegetation. In essence, this technique enables the detection of single trees and their properties in all forest layers. This paper highlights a successful mapping of tree species—subdivided into conifers and broadleaf trees—and standing dead wood in a large forest 924 km2 in size. As a novelty, we calibrate the critical stopping criterion of the tree segmentation based on a normalized cut with regard to coniferous and broadleaf trees. The experiments were conducted in Šumava National Park and Bavarian Forest National Park. For both parks, lidar data were acquired at a point density of 55 points/m2. Aerial multispectral imagery was captured for Šumava National Park at a ground sample distance (GSD) of 17 cm and for Bavarian Forest National Park at 9.5 cm GSD. Classification of the two tree groups and standing dead wood—located in areas of pest infestation—is based on a diverse set of features (geometric, intensity-based, 3D shape contexts, multispectral-based) and well-known classifiers (Random forest and logistic regression). We show that the effect of under- and oversegmentation can be reduced by the modified normalized cut segmentation, thereby improving the precision by 13%. Conifers, broadleaf trees, and standing dead trees are classified with overall accuracies better than 90%. All in all, this experiment demonstrates the feasibility of large-scale and high-accuracy mapping of single conifers, broadleaf trees, and standing dead trees using lidar and aerial imagery.