The morphological and molecular features of Penicillium roqueforti and P. paneum isolated from baled grass silage were characterised. A total of 315 isolates were investigated, comprising 237 P. roqueforti and 78 P. paneum isolates randomly selected from more than 900 Penicillium colonies cultured from bales. The macromorphological features of both species broadly agreed with the literature, but the micromorphological features differed in some respects. When observed using SEM, P. roqueforti and P. paneum had finely roughened conidia, and conidiophores, phialides and conidia of P. paneum were each larger than those of P. roqueforti. Based on the phylogenetic analysis of partial sequences of beta-tubulin and acetyl co-enzyme A (CoA) synthetase genes, P. roqueforti and P. paneum isolates were found to be monophyletic species.