Rear Admiral Travis Sinniah is the first Tamil to head a wing of the military since 1970, even though Tamils make up around 15 percent of Sri Lanka's population.
In 1972, the separatist Tamil Tigers took up arms and launched a bloody guerrilla war for a separate state for the ethnic minority that only ended in May 2009 when they were crushed in a no-holds barred military offensive.
"Rear Admiral Travis Sinniah, who has served Sri Lanka navy with immense loyalty for many decades, took office as the navy commander today," the president said on Twitter.
Sri Lanka's separatist war claimed the lives of at least 100,000 people between 1972 and 2009, according to UN estimates.
The conflict discouraged the mainly Hindu Tamil community as well as Muslims -- Sri Lanka's second largest minority -- from joining the armed forces and police.
Only a few of them remained across the military.
The Tamil Tigers had cited discrimination in jobs and education among the key reasons for their campaign for a separate state.
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