Full details of the 13,500-gene sequence will be published in Nature Biotechnology in October.
The bug, Penicillium chrysogenum, is used in the production of antibiotics such as amoxicillin, ampicillin, cephalexin and cefadroxil.
Its use in killing bacteria was discovered in 1928 after mould spores accidentally contaminated a petri dish in a laboratory.
Further work discovered it was safe for use in humans.
About one billion people are thought take penicillin every year around the world.
But antibiotic resistance is becoming an increasingly serious problem, as for example has been shown with MRSA.
UK experts have repeatedly cautioned against overuse of antibiotics and warned there is an urgent need for industry to develop new drugs.
Researchers said in addition to combating resistance, the genome sequence may also help to improve the manufacturing of antibiotics.
Dr Roel Bovenberg, a researcher at DSM Anti-Infectives, the biotechnology company behind the genome sequencing, said the four-year project had thrown up "several surprises" which they were investigating further in collaboration with academics.
"It provides insight into what genes encode for, know-how in terms of manufacturing and new compounds to be identified and tested.
"There are genes and gene families we did not think would be involved in biosynthesis of penicillins - they weren't on our radar so that is our follow-up work."
Professor Hugh Pennington, an expert in bacteriology at the University of Aberdeen, said the genome sequence might well lead to the development of new antibiotics.
"If we understand the genome we might be able to manipulate the genes."
He said traditionally antibiotics had been found just from looking at what fungi produce, but in recent years scientists had been trying to modify existing treatments, BBC reports.
"All the easy targets have been hit by one drug or another so it's proving very difficult to find new compounds and we're going to need some lateral thinking.
"If the genome helps to do antibiotic development quicker, then that can only be a good thing."