The systematic conservation approach is now commonly used for the design of efficient marine protected area (MPA) networks. Identifying these priority areas often involves using specific conservation-planning software. Several of these software programmes have been developed in recent years, each of which differs in the underlying algorithms used. Here, we investigate whether the choice of software influences the location of priority areas by comparing outputs from Marxan and Zonation, two widely used conservation-planning, decision-support tools. Using biological and socio-economic data from the eastern English Channel, we compared their outputs and showed that the two software packages identified similar sets of priority areas, even though the relatively wide distribution of the habitat types and species considered offered a great deal of flexibility. Moreover, this similarity increased with increasing spatial constraint, especially when using real-world cost data, suggesting that choice of cost metric has a greater influence on conservation-planning analyses than choice of software. However, we found that Marxan generally produced more efficient results and Zonation produced results with greater connectivity, so the most appropriate software package will depend on the overall goals of the MPA planning process.