MetaClassifier is an integrated pipeline for identifying the floral composition of honey using DNA metabarcoding to determine the plants that honey bees visit. MetaClassifier utilizes a database of marker sequences and their corresponding taxonomy lineage information to classify high-throughput metabarcoding sample sequencing reads data into taxonomic groups and quantify taxon abundance. MetaClassifier can also be employed in other studies that utilize barcoding, metabarcoding, and metagenomics techniques to characterize richness, abundance, relatedness, and interactions in ecological communities.