The Geiseltal fossil collection from southern Sachsen-Anhalt Germany contains remarkably well-preserved fossils of middle Eocene age. These include several crocodylian skulls, representing at least four different genera with a fifth genus represented by two mandibular rami. As sites with this many crocodylian genera are unknown in modern ecosystems, it has been hypothesized that these crocodylians may have differences in habit as compared to living crocodylians. In order to test similarities between the Geiseltal crocodylians and extant species, an analysis was conducted using geometric morphometrics to quantify shape in crocodylian skulls of all living species (n = 218) and all well-preserved crocodylian skulls of the Geiseltal fauna (n = 28). A relative warps analysis was used to quantify and compare skull shape, revealing Allognathosuchus and Boverisuchus to be very distinct from each other as well as from Asiatosuchus and Diplocynodon. Overlap in shape alone exists between some Diplocynodon and some Asiatosuchus, but there was significant difference in adult size. When compared with extant crocodylians, three Geiseltal genera occupied distinctly non-modern morphospace in the first two relative warps axes. Comparison of the diets of living crocodylians with similarly shaped skulls was used to reconstruct the prey preferences of the Geiseltal crocodylians, revealing differences in specialization. During the middle Eocene high global temperatures, partitioning of prey preference may have allowed this group to attain its higher than usual diversity, reducing the amount of direct competition.