Byssochlamys and related Paecilomyces strains are often heat resistant and may produce mycotoxins in contaminated pasteurised foodstuffs. A comparative study of all Byssochlamys species was carried out using a polyphasic approach to find characters that differentiate species and to establish accurate data on potential mycotoxin production by each species. Phylogenetic analysis of the ITS region, parts of the P-tubulin and calmodulin genes, macro- and micromorphological examinations and analysis of extrolite profiles were applied. Phylogenetic analyses revealed that the genus Byssochlamys includes nine species, five of which form a teleomorph, i.e. B. fulva, B. lagunculariae, B. nivea, B. spectabilis and B. zollemiae, while four are asexual, namely P. brunneolus, P. divaricatus, P. formosus and P. saturatus. Among these, B. nivea produces the mycotoxins patulin and byssochlamic acid and the immunosuppressant mycophenolic acid. Byssochlamys lagunculariae produces byssochlamic acid and mycophenolic acid and thus chemically resembles B. nivea. Some strains of P saturatus produce patulin and brefeldin A, while B. spectabilis (anamorph P. variotii s.s.) produces viriditoxin. Some micro- and macromorphological characters are valuable for identification purposes, including the shape and size of conidia and ascospores, presence and ornamentation of chlamydospores, growth rates on MEA and CYA and acid production on CREA. A dichotomous key is provided for species identification based on phenotypical characters.