HaeIII along with other restriction enzymes were discovered in 1970 by Werner Arber and Matthew Meselson.

The HaeIII methyltransferase also known as MTase gene from Haemophilus aegyptius (recognition sequence: 5′-GGCC-3′) was made into Escherichia coli (E.coli) in the plasmid vector pBR322.

Clones carrying additional adjacent fragments were found to code for the HaeIII restriction enzyme.

HaeIII cuts both strands of DNA in the same location, yielding restriction fragments with blunt ends.

[2] Haemophilus aegyptius also carries a methylase dubbed HaeIIIM (P20589) that methylates the internal cytosines in the GGCC sequence.