From 1858, Emil Rostrup was a teacher at the paedagogical college Skårup Seminarium in then new subject natural history. He educated to-be school teachers for 25 years. In the meantime he had become well known for his flora handbooks and his works on plant pathology. He was appointed docent at the Royal Veterinary and Agricultural University in 1883. From 1902, he was professor at the same college. Rostrup was first real plant pathologist in Denmark and probably the greatest ever. He was member of Royal Danish Academy of Sciences and Letters (from 1882), Royal Physiographic Society in Lund (from 1888), Royal Swedish Academy of Agriculture and Forestry (from 1890). In 1894, he was made honorary doctor at the University of Copenhagen.