Schmidt was born at
Jægerspris, Denmark, son of Ernst Schmidt and Camilla Ellen Sophie Schmidt (born Kjeldall and sister to the chemist
Johan Kjeldahl). Schmidt began his studies of natural history at the
University of Copenhagen under professor of botany
Eugen Warming (1841–1924), and obtained an MS degree in biology in 1898. He obtained a grant from the
Carlsberg Foundation to study the flora of the coastal areas of
Ko Chang in then
Siam, including both
mangrove trees and
microalgae. He made his doctoral thesis in biology and botany, on shoot architecture of
mangrove trees and
Eugen Warming served as faculty opponent in October 1903. had first been sent to London to be published by the
Royal Society, but was refused with a note that
Grassi's work on the subject sufficed. This constitutes a clear example of
peer review failure. Ten years later, Schmidt's work on the spawning place of the eel was published by the
Royal Society and even later he was awarded the
Darwin Medal.{{cite web|url= https://docs.google.com/spreadsheets/d/1dsunM9ukGLgaW3HdG9cvJ_QKd7pWjGI0qi_fCb1ROD4/pubhtml?gid=216486814&single=true|title = Johannes Schmidt, 1930|website= The Royal Society ==Personal life==