Petersen's main research was in what was then known as lower fungi – Chytridiomycota and Oomycetes, but he also studied the systematics of Red algae. Parallel to these lines of research, he investigated the intraspecific morphological variation in plant species – which would today be called quantitative genetics.
The Oomycete genus Petersenia is named to his honour.
Petersen, H.E. (1903) Notes sur les Phycomycètes observés dans les téguments vides des nymphes de Phryganées avec description de trios espèces nouvelles de Chytridinées. Journal de Botanique 17 (6–7): 214–222.
Petersen, H.E. (1905) Contributions à la connaissance des Phycomycètes marins (Chrytridinæ Fischer). Oversigt over det Kongelige Danske Videnskabernes Selskabs Forhandlinger 1905 (5): 439–488