The Portuguese endemic callipodidan millipede Lusitanipus alternans (Verhoeff, 1893) is redescribed, based on abundant new material collected in caves of central Portugal. The species is illustrated with comprehensive SEM images. The relationships of the genus Lusitanipus Mauriès, 1978 to other callipodidan genera of the subfamily Cyphocallipodinae Verhoeff, 1909 are discussed. The major part of the studied material is highly infected with ectoparasitic fungi of the order Laboulbeniales, we also include information about the infection in the subterranean ecosystem.