This article describes an exemplar-based approach to species checklist alignment. Biologists in many fields often work with tables whose rows denote taxonomic groups (more formally called taxonomic concepts). Such tables, here called checklists, are essential ingredients for communicating the information contained in many research articles, databases developed for research projects and laboratories and comprehensive taxonomic resources, such as the Mammal Diversity Database and Catalogue of Life. An important activity is reconciling or aligning two or more checklists (also called taxonomic concept mapping), i.e. relating the records of one checklist to the records of another. Our implementation of exemplar-based alignments is scalable both pragmatically and computationally: it does not require labour-intensive manual processing of the checklists or alignments, it handles large checklists efficiently and it is usefully aware of taxonomic concept relationship mappings. Open-source code implementing the exemplar-based approach is available online as part of the List Tools software library.