Naturally occurring manganese (₂₅Mn) is composed of one stable isotope, ⁵⁵Mn. 26 radioisotopes have been characterized, with the most stable being ⁵³Mn with a half-life of 3.7 million years, ⁵⁴Mn with a half-life of 312.3 days, and ⁵²Mn with a half-life of 5.591 days. All of the remaining radioactive isotopes have half-lives that are less than 3 hours and the majority of these have half-lives that are less than a minute. This element also has 3 meta states.

Manganese is part of the iron group of elements, which are thought to be synthesized in large stars shortly before supernova explosions. ⁵³Mn decays to ⁵³Cr with a half-life of 3.7 million years. Because of its relatively short half-life, ⁵³Mn occurs only in tiny amounts due to the action of cosmic rays on iron in rocks. Manganese isotopic contents are typically combined with chromium isotopic contents and have found application in isotope geology and radiometric dating. Mn−Cr isotopic ratios reinforce the evidence from ²⁶Al and ¹⁰⁷Pd for the early history of the Solar System. Variations in ⁵³Cr/⁵²Cr and Mn/Cr ratios from several meteorites indicate an initial ⁵³Mn/⁵⁵Mn ratio that suggests Mn−Cr isotopic systematics must result from in-situ decay of ⁵³Mn in differentiated planetary bodies. Hence ⁵³Mn provides additional evidence for nucleosynthetic processes immediately before coalescence of the Solar System.

The isotopes of manganese range in atomic weight from 46 u (⁴⁶Mn) to 72 u (⁷²Mn). The primary decay mode before the most abundant stable isotope, ⁵⁵Mn, is electron capture and the primary mode after is beta decay.