Hilgendorf's research on fossil snails from the Steinheim crater in the early 1860s became a palaeontological evidence for the theory of evolution published by Charles Darwin in 1859.

In 1868, Hilgendorf became director of the aquarium of the Zoological Garden of Hamburg and in 1870 and 1871 he worked as librarian at the German Academy of Sciences Leopoldina.

He stayed in Japan from 1873 till 1876 and published articles and collected several specimens of Japanese fauna.

[1] In 1890 Gustav Wilhelm Müller identified a new species of ostracod crustacean in the collection of Hilgendorf and named it Cypridina hilgendorfii.

[1][4] His 1866 publication which described the phylogeny of Planorbis multiformis in detail has been described as "one of the most important contributions of paleontology to early Darwinism".

[4] Darwin acknowledged the findings of Hilgendorf and referred to his research in the sixth edition of On the Origin of Species, 1872.