Forward genetic screens have elucidated molecular pathways required for innumerable aspects of life, however identifying the causal mutations from such screens has long been the bottleneck in the process, particularly in vertebrates. We have developed an RNA-Seq based approach that identifies both the region of the genome linked to a mutation and candidate lesions that may be causal for the phenotype of interest. We show that our method successfully identifies zebrafish mutations that cause nonsense or missense changes to codons, alter transcript splicing, or alter gene expression levels. Furthermore, we develop an online accessible or downloadable bioinformatics pipeline allowing for easy implementation of all steps of the method. Overall, we show that RNA-Seq is a fast, reliable, and cost effective method to map and identify mutations that will greatly facilitate the power of forward genetics in vertebrate models.