An aerobic, Gram negative extracellular agarase producing bacillus was discovered in Taitung, Taiwan. It has a small plasmid containing an agarase gene with high enzyme activity. This bacterium was identified as Alcaligenes sp. strain Yen (AY744384) by 16S RNA sequencing comparison and MicroScan-AS4 automatic microorganism analyzing data. The intact plasmid was successfully transformed into competent E. coli HB 101 cells for the first time. The enzyme was purified from culture supernatant. The enzyme had a specific agarase activity of 406 U/mg. The plasmid was estimated 18.4 kb by comparing to electrophoresis markers. This agarase couldn’t degrade ι-carrageenan and κ-carrageenan, but could degrade sodium alginate. The enzyme’s acting target was β-1,4 bond, so, the enzyme was recognized as β type. This is a discovery of a previously undescribed small agarolytic plasmid and the first time transformation of the intact agarase gene containing plasmid into E.coli. Some enzyme characteristics were also described.