Globally, protected areas are being established to protect biodiversity and to promote ecosystem resilience. The typical spatial conservation planning process leading to the creation of these protected areas focuses on representation and replication of ecological features, often using decision support tools such as Marxan. Yet, despite the important role ecological connectivity has in metapopulation persistence and resilience, Marxan currently requires manual input or specialized scripts to explicitly consider connectivity. ‘Marxan Connect’ is a new open source, open access Graphical User Interface (GUI) tool designed to assist conservation planners with the appropriate use of data on ecological connectivity in protected area network planning. Marxan Connect can facilitate the use of estimates of demographic connectivity (e.g. derived from animal tracking data, dispersal models, or genetic tools) or structural landscape connectivity (e.g. isolation by resistance). This is accomplished by calculating metapopulation-relevant connectivity metrics (e.g. eigenvector centrality) and treating those as conservation features or by including the connectivity data as a spatial dependency amongst sites in the prioritization process. Marxan Connect allows a wide group of users to incorporate directional ecological connectivity into conservation planning with Marxan. The solutions provided by Marxan Connect, combined with ecologically relevant post-hoc testing, are more likely to support persistent and resilient metapopulations (e.g. fish stocks) and provide better protection for biodiversity.