Background Large genotyping datasets have become commonplace due to efficient, cheap methods for SNP identification. Typical genotyping datasets may have thousands to millions of data points per accession, across tens to thousands of accessions. There is a need for tools to help rapidly explore such datasets, to assess characteristics such as overall differences between accessions and regional anomalies across the genome. Results We present GCViT (Genotype Comparison Visualization Tool), for visualizing and exploring large genotyping datasets. GCViT can be used to identify introgressions, conserved or divergent genomic regions, pedigrees, and other features for more detailed exploration. The program can be used online or as a local instance for whole genome visualization of resequencing or SNP array data. The program performs comparisons of variants among user-selected accessions to identify allele differences and similarities between accessions and a user-selected reference, providing visualizations through histogram, heatmap, or haplotype views. The resulting analyses and images can be exported in various formats. Conclusions GCViT provides methods for interactively visualizing SNP data on a whole genome scale, and can produce publication-ready figures. It can be used in online or local installations. GCViT enables users to confirm or identify genomics regions of interest associated with particular traits. GCViT is freely available at https://github.com/LegumeFederation/gcvit. The 1.0 version described here is available at https://doi.org/10.5281/zenodo.4008713.