Ali Manikfan was born to Musa Manikfan and Fatima Manika in Minicoy Island of Lakshadweep on 16 March 1938. His father Musa sent him to Kannur for formal education. As he was not interested in formal education, he left his studies and returned to his home land. According to him formal education is artificial and pointless and best way to acquire knowledge is getting wisdom by observing our environment.

As a polyglot, Ali Manikfan knows a great number of languages. Besides his mother tongue Divehi (Mahl), he learned English, Hindi, Malayalam, Arabic, Latin, French, Russian, German, Sinhalese, Persian, Sanskrit, Tamil and Urdu. His other areas of interest are marine biology, marine research, geography, astronomy, social science, traditional shipbuilding, education, fisheries, agriculture and horticulture.

In 1956 he worked as a teacher and then became a clerk in Minicoy. (Indian government's chief civil official on the Island). However, his interest was in marine life - in the 1960s he joined the Central Marine Fisheries Research Institute of India.