Extending ecological research back through deep time provides an important framework for understanding the macroevolutionary context of the structure, function, and dynamics of today’s and tomorrow’s ecosystems. While many paleoecological studies focus on species morphology, diversity, and distributions, there are also opportunities to analyze complex species interactions. We have compiled detailed food webs for ancient ecosystems from ~500 and 50 million years before present. Using various network structure analysis and modeling techniques developed in the last decade of research on extant systems, including the recently developed probabilistic niche model and MaxEnt analyses of link distributions, we assess the organization of these paleo-food webs with comparisons to current ecosystems. The implications for system constraints and robustness are considered.