Paleontologists are increasingly concerned with understanding the biology of extinct species and their environments. This has resulted in a proliferation of new techniques and methodologies that provide a wealth of new data for understanding the paleobiology of extinct species and paleoecological relationships between them and their environment. However, combining such analyses to reconstruct an ancient terrestrial ecosystem can present many challenges, particularly when different lines of evidence appear to provide contradictory information. Here, we discuss some of the ways that taphonomy can bias primary data and how awareness of such issues can increase the accuracy of paleoecological studies. We discuss two geographically and temporally disparate fossil sites as examples of paleoecological reconstruction (the Pliocene of East Africa and the early Oligocene of central Chile) and possible ways of reconciling apparently contradictory data and analyses. We conclude that reconstructing ancient ecosystems requires: (1) accurate data and knowledge of potential biases; (2) a thorough understanding of the analytical techniques being applied and their a priori assumptions; and (3) a willingness to recognize non-analog species, habitats, and communities when necessary.