The winners will be announced at the athletics awards on November 24.
The International Athletics Federation (IAAF) included Russia's high jumper Mariya Lasitskene in the list of female nominees for the IAAF's Athlete of the Year award.
Van Niekerk‚ who retained his 400m title in London‚ and long-jump champion Manyonga‚ whose 8.65m national record was also the best jump this decade so far‚ are among 10 candidates for the men's award.
Kenya's 5,000m victor Hellen Obiri, Australia's 100m hurdles gold medallist Sally Pearson and South African 800m champion Caster Semenya are the other track nominees on the shortlist.
The Kenyan duo had a stellar 2017 season where both won gold medals at the IAAF World Championships in London with Obiri adding the women's 5000m Diamond League trophy to her collection of 2017 awards.
Everyone named won gold medals at this year's IAAF World Championships, held in London in August.
Bolt, an eight-time Olympic champion, won the 2016 prize and has claimed the award six times in all.
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It listed the male nominees to include Mutaz Barshim of Qatar, Elijah Manangoi of Kenya, Pawel Fajdek of Poland, Mohamed Farah of Great Britain and Sam Kendricks of the US.
The list of 10 men and 10 women nominees were selected by an worldwide panel.
Fans can vote on the IAAF's social media platforms‚ with their poll counting 25%.
Monday marked the opening of a three-way voting process, from the IAAF Council, the IAAF Family and fans, until the closure on October 16.
The IAAF Council's vote will count for 50% of the result, while the IAAF Family's votes and the public votes will each count for 25% of the final result.
Individual graphics for each nominee will be posted on the IAAF's Facebook and Twitter profiles later this week. At the conclusion of the voting process, three men and three women finalists will be announced by the IAAF.
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