22 November 2015 Last updated at 05:46 GMT
Zimasa Mabela broke new ground when she took charge of a de-mining ship based in Cape Town last month.
The 38-year-old mother of two says she wants to be judged on her ability to command and not her gender.
The BBC's Nomsa Maseko spent the day with her on her ship.
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The first African woman to command a navy vessel has recently been appointed in South Africa.