Ernst Hallier (15 November 1831, in Hamburg – 19 December 1904, in Dachau) was a German botanist and mycologist.
As a young man he was trained as a gardener, later studying botany at the universities of Berlin, Jena and Göttingen.
Hallier claimed that many diseases were caused by fungi including cholera, typhoid and measles.
He claimed that he had extracted the causal fungi from patients but other scientists found that this was merely a case of external contamination.
He was also responsible for a revision of Schlechtendal, Langethal & Schenk's "Flora von Deutschland" (5th edition, Gera 1880–88, 30 volumes).