Geographic information systems (GIS) have become more suitable for online delivery. But teaching GIS online is challenging because, without enough interactions with the instructor or among themselves, students may not understand processes, use critical thinking, and collaborate effectively on a team project. This study aims to evaluate two online visual collaboration tools, Padlet and Conceptboard, in enhancing learner engagement, collaboration, and visual communication in an online GIS course. We analyze 1) usage patterns and their relationship with student performance, 2) students' opinions on the added values of the tools compared with face-to-face delivery, and 3) students' qualitative feedback. Student findings show that those tools, particularly Conceptboard, help students get timely help from other students and the instructors, be motivated by participating in discussions and seeing others' progress, organize and brainstorm project ideas, and summarize and present the final products. The combination of Conceptboard and an online video conference tool is a particularly effective alternative to the face-to-face learning environment. On the other hand, we also found significant challenges with remote teamwork in GIS. The course design incorporating online collaboration tools can provide practical strategies to instructors who teach GIS or similar software online.