Botrychium tunux and Botrychium yaaxudakeit, new species of moonworts currently known only from southern Alaska, are described and illustrated. These ferns are distinguished from B. lunaria, with which they have been confused, by allozyme data and their morphological characteristics. Ploidy levels of B. tunux (diploid) and B. yaaxudakeit (tetraploid) are inferred from allozyme patterns. A key to Alaskan moonworts is presented.