Abstract Summary Bionano optical mapping is a technology that can assist in the final stages of genome assembly by lengthening and ordering scaffolds in a draft assembly by aligning the assembly to a genomic map. However, currently, tools for visualization are limited to use on a Windows operating system or are developed initially for visualizing large-scale structural variation. MapOptics is a lightweight cross-platform tool that enables the user to visualize and interact with the alignment of Bionano optical mapping data and can be used for in depth exploration of hybrid scaffolding alignments. It provides a fast, simple alternative to the large optical mapping analysis programs currently available for this area of research. Availability and implementation MapOptics is implemented in Java 1.8 and released under an MIT licence. MapOptics can be downloaded from https://github.com/FadyMohareb/mapoptics and run on any standard desktop computer equipped with a Java Virtual Machine (JVM). Supplementary information Supplementary data are available at Bioinformatics online.