Many of the buildings of the botanic garden were constructed in the Meiji and Taisho periods (the late 19th and early 20th centuries). There are six building that were designated as Important Cultural Properties in 1989: i.e., Museum (built in 1882 and the oldest among museum buildings being used in Japan), Ex-Administrative Office (1900), Museum Storeroom (1885), Museum Restroom (1903), Museum Aviary (1924), and Gate House (1911). Only the museum and the museum restroom are open to the public and the others can only be viewed from the exterior.

　In the botanic garden, there are two building that were designated as Registered Tangible Cultural Properties of Japan in 2000: i.e., Miyabe Kingo Memorial Building and Batchelor Memorial Building.
　Miyabe Kingo Memorial Building was built in 1901 as a lecture hall for zoology and botany in the campus of Sapporo Agricultural College (current Hokkaido University) and relocated at the present place in 1942. Thereafter, it was used as a main office building of the botanic garden until recently. The building displays items related to Prof. Miyabe, including his notebooks during college, field notes recording plant collections, microscope, etc.
　Batchelor Memorial Building, constructed in 1898 and relocated at the present place in 1962, is a former residence of an English missionary John Batchelor (1855-1944). He lived among the Ainu communities and worked on the education of the Ainu and research on the Ainu language. The building houses items left by him, but it is not open to the public and can only be viewed from the exterior.

　A big Ainu dugout canoe is made of a log of Manchurian ash and was used for fishing and transportation in lakes and marshes. The dugout canoe was designated as Important Tangible Folk-cultural Property of Japan in 1957. The dugout is exhibited in Northern Peoples Museum.