He was born in Sachsenberg (now part of Schwerin) as the fifth child and only son of the psychiatrist Carl Friedrich Flemming (1799–1880) and his second wife, Auguste Winter.

He identified that chromatin was correlated to threadlike structures in the cell nucleus – the chromosomes (meaning coloured bodies), which were named thus later by German anatomist Wilhelm von Waldeyer-Hartz (1841–1923).

He studied mitosis both in vivo and in stained preparations, using as the source of biological material the fins and gills of salamanders.

Flemming was unaware of the work of Gregor Mendel (1822–84) on heredity, so he did not make the connection between his observations and genetic inheritance.

[6] Flemming's name is honoured by a medal awarded by the German Society for Cell Biology (Deutsche Gesellschaft für Zellbiologie).