Scarecrow's Thugs were a gang of criminals, in part a combination of shanghaied gangsters and mentally-ill patients and guards of Arkham Asylum, who served under Dr. Jonathan Crane/the Scarecrow.
Inmates of Arkham Asylum helped Dr. Crane dump barrels of his fear toxin into the water pipes running under the building, a plan to unleash it on the citizens of Gotham City. Several of them entered combat with Batman when he showed up to rescue Rachel Dawes.
In a business dealing with the Chechen, Dr. Crane, who now identified himself as Scarecrow, brought several armed thugs for security. They came under siege by the Batmen, and finally Batman himself.