Micromammals, particularly rodents, are important paleoenvironmental indicators and their investigation has the potential to deliver a large amount of invaluable information for the interpretation of archeological sites and past environments. Data from paleogenetic and paleogenomic analyses of this important resource could contribute substantially to these interpretations. Most rodent remains, however, originate from accumulations through predators, such as pellets of raptors. In modern pellets, we could show that the passage of rodents through the digestive tract heavily damages DNA in their bones and teeth although the extent of DNA damage depends on the location of the remains in the stomach of the predator and the duration they are subject to the attack of the gastric juices. Thus, a minute portion of DNA can be rather well preserved. It is likely that it is this portion that is prone to long-term preservation since we could show DNA to be preserved in rodent remains from the El Harhoura2 cave in Morocco in levels dated to ca. 6,000 and 44,000 years. We also performed experiments of monitored taphonomy and analyzed DNA degradation and the transformation of the microbiome in bones of mice buried for different time intervals covering a period of 2 years. These experiments shed light on the processes through which biological specimens turn into environmental specimens.