Steindachner's reputation as an ichthyologist grew, and in 1868 he was invited by Louis Agassiz to accept a position at the Museum of Comparative Zoology at Harvard University. Steindachner took part in the HasslerExpedition of 1871-1872. In 1874 he returned to Vienna and in 1887 was appointed director of the Zoological Department of the Naturhistorisches Museum. In 1898 he was promoted to director of the museum.
Steindachneridion, a genus of fish in South America discovered by Steindachner, is named after him.