MOTIVATION: Synteny analysis is a widely used framework in comparative genomics studies, which provides valuable information to reveal chromosome collinearity in both intra-species and inter-species. Most analysis pipelines, however, are command line-based, making it challenging for biologists to run the algorithms and visualize the results. Existing visualization tools either provide static plots or can only be run on web-based servers and lack efficient visualization methods for associating macro-synteny blocks with individual gene pairs in a micro-synteny region. RESULTS: We developed ShinySyn, a Shiny/R application built on the MCscan framework that provides an easy-to-use graphic interface for synteny analyses without requiring any programming skills, to reduce technical barriers. ShinySyn not only provides interactive visualization for macro-synteny, micro-synteny and genome-level dot views, but it also creates an intuitive representation with a dynamic zooming feature from macro-synteny to individual homologous genes. AVAILABILITY AND IMPLEMENTATION: The source code and installation instructions for ShinySyn can be accessed via https://github.com/obenno/ShinySyn. A pre-built docker image is also available at https://hub.docker.com/r/obenno/shinysyn. The application can be used locally or seamlessly integrated into any Shiny application server.