Although heteroplasmy has been studied extensively in animal systems, there is a lack of tools for analyzing, exploring and visualizing heteroplasmy at the genome-wide level in other taxonomic systems. We introduce icHET, which is a computational workflow that produces an interactive visualization that facilitates the exploration, analysis, and discovery of heteroplasmy across multiple genomic samples. icHET works on short reads from multiple samples from any organism with an organellar reference genome (mitochondrial or plastid) and a nuclear reference genome.