The pterosaurs were the first vertebrates to evolve powered flight and they staged a major radiation in the Cretaceous. Cretaceous pterosaurs occupied many of the niches occupied today by birds, including aerial insect hawkers, piscivores, and filter feeders. The diversity of this radiation remains poorly known due to the uneven stratigraphic and geographic distribution of pterosaur fossils. Much of what is known about pterosaur diversity comes from a handful of Lagerstätten, representing primarily lacustrine, lagoonal, and marine palaeoenvironments, primarily in Laurasia. These sites may fail to capture pterosaur diversity in other habitats and regions, such as Gondwana. Here, we describe a unique small, long-beaked pterosaur, Leptostomia begaaensis gen. et sp. nov., from fluvial mid-Cretaceous (?Albian–Cenomanian) strata of Morocco, North Africa, with adaptations for sediment probing. The upper and lower jaws form a hyperelongate dorsoventrally flattened beak, with thickened bony walls. The morphology most closely resembles that of probing birds such as kiwis, ibises, and curlews that probe in mud or earth for invertebrates. The affinities of the new pterosaur are unclear. It likely represents an azhdarchoid, but does not clearly fit within any known azhdarchoid clade. The new pterosaur adds to the remarkable diversity of pterosaurs known from the mid-Cretaceous, and suggests that pterosaur diversity remains under sampled.