In 1862 he founded the Società dei Naturalisti Modenesi (Modena Society of Naturalists), and in 1871, the Società Veneto-Trentina di Scienze Naturali (Trento-Venetian Society of Natural Sciences). He is credited with establishment of the bacteriology laboratory at Padua.
Canestrini made contributions in several biological disciplines, performing important research in the field of acarology. He was an advocate of Darwinism, and was responsible for translating Darwin's works into Italian. Through these translations, Canestrini was a principal factor concerning the popularity of Darwinism in 19th century Italy. During his career he was the author of almost 200 scientific publications.