Mookerjee is a surname. Notable people with the surname include:
Harendra Coomar Mookerjee (1877–1956), the Governor of West Bengal from 1951 to 1956 Rajen Mookerjee, KCIE, KCVO, a pioneering Indian industrialist Syama Prasad Mookerjee (1901–1953), minister in Pandit Jawaharlal Nehru's Cabinet as a Minister for Industry and Supply
See also Mukherjee, one of several alternative spellings, for a full discussion of the history of the name
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