Protected areas (PAs) are among the main tools for preserving biodiversity and creating an environment for the natural course of ecological processes. The identification of forest biodiversity is especially important for large metropolitan areas. An obvious problem in assessing the efficiency of the PAs network is the lack of up-to-date cartographic materials representing the typological diversity of vegetation. The aim of the paper is to identify forest biodiversity and fragmentation in the example of the Moscow region (MR)—the largest metropolis in Eastern Europe. The typological classification was carried out at a detailed hierarchical level—33 association groups (ass.gr.) considering the diversity of the land cover. A random forest algorithm was used for cаrtographic mapping (overall accuracy 0.59). Remote sensing (RS) data included Sentinel-2A, DEM SRTM, and PALSAR radar images. Six fragmentation metrics were calculated based on the raster map of forest typological diversity. A significant correlation between the forest diversity and PAs forest patch fragmentation metrics was noted. It has been established that the PAs proportion of the territory accounts for almost 20% only within the northernmost district and noticeably decreases to the south to 1–2%. At the same time, fragmentation noticeably increases from Northeast to Southwest. The category of PAs does not affect the state of the forest cover. Additionally, there was no direct influence of the anthropogenic factor from both local sources and a large regional source, i.e., the city of Moscow. It is shown that the average area of PAs, supporting 75% of the typological diversity of regional communities, was about 1000 ha. The results of the study suggest that there is a general lack of environmental protection measures in the region. It is recommended to increase the area of PAs, primarily for less fragmented forest patches, including indigenous forest-steppe and forest types of communities.