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 systems such as Marxan. Unfortunately, Marxan currently requires manual input or specialised scripts to explicitly consider ecological connectivity, a property critical to metapopulation persistence and resilience. "Marxan Connect" is a new open source, open access Graphical User Interface (GUI) designed to assist conservation planners in the systematic operationalization of ecological connectivity in protected area network planning. Marxan Connect is able to incorporate estimates of demographic connectivity (e.g. derived from tracking data, dispersal models, or genetics) 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 using the connectivity data as a spatial dependency amongst sites to be included in the prioritization process. Marxan Connect allows a wide group of users to incorporate directional ecological connectivity into conservation plans. The least-cost conservation 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 than if connectivity is ignored.