Accurately recognizing analogs between fossil and modern ecosystems allows paleoecologists to more fully interpret fossil assemblages and modern ecologists to leverage the fossil record to address long-term ecological and environmental changes. However, this becomes increasingly difficult as taxonomic turnover increases the dissimilarity between ecosystems. Here we use a guild-based approach to compare the ecological similarity between Cretaceous cold-seep assemblages preserved in the Pierre Shale surrounding the Black Hills and modern cold-seep assemblages from five previously recognized biofacies. We modify modern assemblage data to include only those taxa with fossilizable hardparts greater than 5 mm in length to make these modern datasets more comparable to potential fossil analogs. We find that while the Black Hills assemblages are more similar in ecological guild composition to the modern thyasirid biofacies, subsets share similarities in ecological structure to the lucinid and mussel bed biofacies. The fossil seep assemblages are also more similar to each other than are modern assemblages belonging to the same biofacies, despite greater geographic and temporal dissimilarity among the fossil samples. Furthermore, guild-level ordination analyses show a secondary faunal gradient that reflects community succession in the hard-substrate dominated modern assemblages and reveals a parallel faunal gradient in the soft-sediment dominated Cretaceous assemblages, consistent with a gradient in the influence of seep fluids on the faunas. Thus, while the Black Hills assemblages are quite homogeneous in their composition, they capture ecological variation similar to successional patterns in modern seep systems.