Habitat fragmentation is a major threat to biodiversity, but existing literature largely ignores naturally patchy ecosystems in favor of forests, where deforestation creates spatially distinct fragments. Here, we use savannas to highlight the problems with applying forest fragmentation principles to spatially patchy ecosystems. Identifying fragmentation using landscape functionality, specifically connectivity, enables better understanding of ecosystem dynamics. Tools and concepts from connectivity research are well suited to identifying barriers other than vegetation structure contributing to fragmentation. Opportunities exist to improve fragmentation mapping by combining remote-sensing data with field measurements related to connectivity to empirically test whether landscapes are functionally fragmented. Advancements in deep learning and increasingly accessible data open many possibilities for comprehensive maps of fragmentation.