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A new generation of tools that identify fusion genes in RNA-seq data is limited in either sensitivity and or specificity. To allow further downstream analysis and to estimate performance, predicted fusion genes from different tools have to be compared. However, several factors complicate genomic location-based matching in a transcriptome context. FusionMatcher (FuMa) is a program that reports identical fusion genes based on gene-name annotations. FuMa automatically compares and summarizes all combinations of two or more datasets in a single run, without additional programming necessary. FuMa uses only one single gene annotation, avoiding mismatches caused by tool specific gene annotations. Furthermore, FuMa accepts intermediate output files that allow a step wise analysis of corresponding tools.