The Malindi Museum is a museum located in Malindi, Kenya. The museum features temporary exhibits including famous Malindi Coelacanth.

The museum is located in the two story building dating from 1891 also known as House of Columns. It has terraced roof and veranda and for many years served as the first hospital of Malindi. On the east facade there is a colonnade featuring five round pillars. The architecture of the building is similar to that of the former Malindi District Commissioner building erected in 1890. In 1999 the House of Columns was transferred to the National Museum of Kenya and a restoration opened in 2004 as museum.

The Malindi District Commissioner building has been housing Ethnographic Museum of coastal Kenya since 2009.