Both bowlers won their 10th centre titles and added a bar to their Dunedin gold star last season.
This was a significant achievement, with Thomson (57) being only the 23rd male bowler to achieve the feat and Hynes (69) the ninth female.
The annual Bowler of the Year award is decided on a points system from major local events.
Thomson won the Stan Seear Trophy in a close contest with his Fairfield club mates Mark Cowan and Blair Barringer, who also had 14 points.
Thomson won on the countback because he also qualified for post-section play in the three other events,compared with the two by Cowan and one by Barringer.
Thomson also won the Bowler of the Year award in 2000.
Thomson, who started playing bowls at Alexandra in 1985, won his first centre title with Ken Walker as his skip in the open fours in 1991. His 10th title came in the champion of champions triples last season when Fairfield beat Dennis Leeden's Wakari combination 20-19.
He has also been runner-up in centre events seven times.
Thomson is a key member of the Professional Bowls Association and has competed in two international finals in the United Kingdom.
Hynes won her 10th Bowls Dunedin title in the champion of champions triples.
This was the third title of the season for Hynes, who also won the open singles and the open triples.
She won the national fours title in 2003. Hynes (nee Potbury), a former cashier at the School of Dentistry, has played bowls for the past 15 years.
"My husband died suddenly 18 years ago and friends invited me to play bowls," she said.
"It took me three years to come to terms with his death before I started bowls," she said.
The sport helped to lift Hynes' spirits.
"I just love the game," she said. "There are challenges, both indoors and outside."
It was a remarkable effort to win 10 Bowls Dunedin titles in just eight years.
She won the Millie Khan Memorial Trophy with 28 points and was followed by Taieri bowlers Jan Barclay and Janet Swallow, who finished second equal on 16 points.
Hynes won the open singles and triples and the champion of champions triples and was runner-up in the Community Trust fours.
Special mention was made of Bruce Malcolm, who selected the New Zealand men's team that won the Leonard Trophy for the first time at World Bowls in Christchurch last January.
The following bowlers received a bar for their gold stars: Ken Walker (Fairfield), 30 titles, Carolyn Crawford (St Clair), 10 titles.
Gold stars for winning five titles were presented to Blair Barringer (Fairfield) and Andrew McCallum (Leith).
