The three-time FIFA player of the year is a marketing juggernaut with a new Nike deal worth $13 million annually plus endorsement partners such as Tag Heuer and Herbalife plus his own lines of suits, cologne, shirts, shoes, underwear and hotels.
Messi, who sat out Argentina's opening victory at the Copa America Centenario this week, was next at $81.4 million, with $28 million of that from sponsorships.
LeBron James, who leads the Cleveland Cavaliers against defending champion Golden State in the ongoing NBA Finals, was third on the list and tops among Americans with $77.2 million. He has endorsement deals of $54 million, including a lifetime pact with Nike that could pay off to the tune of $1 billion, and $23.2 million in club salary.
James made his movie debut in "Trainwreck" last year and is set to star in the sequel to the 1996 Michael Jordan film "Space Jam" as well as take a huge salary boost next year when the NBA's new $24 billion television deal starts.
Golden State's Stephen Curry, the NBA Most Valuable Player and scoring champion, shared 69th on $23.6 million with world number one golfer Jason Day of Australia.
Roger Federer, the Swiss tennis star with a record 17 men's Grand Slam singles titles, was fourth on $67.8 million. He set the pace in sponsor income at $60 million.
- Top 100 make $3.15 billion -
Television rights fee hikes helped fuel team sport stars, boosting the top-100 cut-off to $20.8 million, $2 million more than last year. The study time frame runs for the 12 months ending one week ago.
The top 100 include 65 Americans and athletes from 22 other nations encompassing 10 sports, with the most from baseball at 26. Together the top 100 took home a combined $3.15 billion, 29 per cent of it from endorsements and appearances.
The 2015 leaders, Mayweather and Filipino icon Manny Pacquiao, both sank with the end of their ring careers. Mayweather dipped to 16th with $44 million in earnings while Pacquiao was 63rd at $24 million.
World number one Serena Williams, runner-up at this years French and Australian Opens, was the highest earning woman at $28.9 million, 40th overall, with doping-banned Russian tennis star Maria Sharapova 88th on $21.9 million.
Sixth overall on the list was Serbian Novak Djokovic, who cracked the top 10 for the first time at $55.8 million, with $34 million in endorsements. Djokovic won the French Open last Sunday to claim his fourth consecutive men's Grand Slam singles title and complete a career Grand Slam.
Kobe Bryant, the Los Angeles Lakers star who retired after this past season, was 10th on $50 million, evenly split between salary and sponsorships.
British Formula One racer Lewis Hamilton was 11th on $46 million, only $4 million from endorsements.
Former world number one Woods, a 14-time major golf champion, was 12th on $45.3 million, all but about $274,000 of it from sponsorship deals.
Northern Ireland golfer Rory McIlroy was 17th at $42.6 million, Spanish tennis star Rafael Nadal and Brazilian footballer Neymar shared 21st at $37.5 million.
Jamaica's Usain Bolt, who seeks more Olympic athletics sprint gold in two months at Rio, was 32nd at $32.5 million.
FORBES' HIGHEST PAID ATHLETES 2016
1. Cristiano Ronaldo - $88 million
2. Lionel Messi - $81.4 million
3. LeBron James - $77.2 million
4. Roger Federer - $67.8 million
5. Kevin Durant - $56.2 million
6. Novak Djokovic - $55.8 million
7. Cam Newton - $53.1 million
8. Phil Mickelson - $52.9 million
9. Jordan Spieth - $52.8 million
10. Kobe Bryant - $50 million
11. Lewis Hamilton - $46 million
12. Tiger Woods - $45.3 million
13. Eli Manning - $45 million
14. Joe Flacco - $44.5 million
15. Tom Brady - $44.1 million
16. Floyd Mayweather - $44 million
17. Rory McIlroy - $42.6 million
18. Russell Wilson - $41.8 million
19. Sebastian Vettel - $41 million
20. Philip Rivers - $38 million