This repository contains mean annual occupancy estimates for 595 saproxylic beetle species and 216 buttefly species (Papilionoidea, incl. Zygaenidae moths) in six biogeographic zones in Switzerland. The data cover the years 1930–2021 (occupancy estimates were determined per two-year interval; 1930/31, 1932/33, etc.). Mean occupancy denotes the average number of 5 km x 5 km squares occupied by the focal species in a zone. Occupancy estimates are derived from occupancy-detection models that were based on species record data which is hosted and curated by info fauna (metadata available from GBIF through https://doi.org/10.15468/cjmjy2 and https://doi.org/10.15468/atyl1j). Data on the level of single Markov chain Monte Carlo (MCMC) iterations of model fitting are included (4,000 sampling iterations). The six biogeographic zones were defined based on biogeographic regions and elevation (squares with a mean elevation above 1,400 m asl are summarised in the "HighAlps" zone).