Tools for the identification of unique multilocus genotypes when both genotyping error and missing data may be present. Includes a data pre-screening utility to analyze pairwise locus overlap and protect against underlying mathematical sorting constraints. Targeted for use with large datasets and databases containing multiple samples of each individual (a common situation in conservation genetics, particularly in non-invasive wildlife sampling applications). Functions explicitly incorporate missing data and can tolerate allele mismatches created by genotyping error. If you use this package, please cite the original publication in Molecular Ecology Resources (Galpern et al., 2012), the details for which can be generated using citation('allelematch'). The complete user manual and analytical tutorials are included locally as an R vignette and can be accessed within an active R session using vignette('allelematch').