This marks Harper's first election since winning power in 2006 without his loyal former finance minister at his side.
Flaherty, who died last year, was a strong communicator, a troop-rallying campaigner and a politician whose international reputation was thought to have helped burnish the party's ever-crucial economic record.
He died suddenly in April 2014 only weeks after leaving his finance minister's post.
While former high-profile ministers like John Baird, Peter MacKay and James Moore have decided not to seek re-election, Flaherty's absence could be felt even more.
He had long given the Conservatives a big name in the Greater Toronto Area, which is once again a critical battleground in the Oct. 19 election.
Flaherty wrestled the Oshawa-Whitby riding from the Liberals in 2006, which gave the party a key Toronto-area foothold. He also held provincial and federal offices in the area for two decades.
Over those years, Flaherty provided a strong presence for conservatives throughout Toronto and helped new candidates establish themselves, former cabinet colleague Chris Alexander said in an interview.
"We have a lot more firepower in terms of incumbent MPs from the GTA because of our success in 2011 and all of that is part of the Jim Flaherty legacy," said Alexander, one of those rookie candidates in 2011 who later became immigration minister.
"He was a natural, effective campaigner, but also a larger-than-life figure for all of Canada — but especially in the Durham region (of Toronto)."
Alexander is seeking re-election in Ajax, the riding close to Flaherty's old district. He said he and Flaherty, who at one time had represented a provincial riding that overlapped Ajax, shared organizers and a network.
"We all miss him and especially in this electoral context, which he loved so much," said Alexander.
Baird, who left politics to join the private sector after managing key dossiers such as foreign affairs, said in a brief statement that his former cabinet colleague was Harper's "Toronto point man."
"Jim was Harper's most credible cabinet minister with experience," said Baird, who has campaigned for Tory candidates in the Toronto area, even though he's not running for re-election.
Beyond Flaherty's regional impact, Harper likely misses his former lieutenant's effective communication skills on economic issues, especially during uncertain times.
The ongoing campaign is unfolding amid a struggling economy, battered by the sharp drop in oil prices and the failure of other sectors to pick up the slack. As a result, it shrank over the first five months of 2015 and some argue the country slipped into recession.
Flaherty earned credibility by managing the finance portfolio through the Great Recession of 2008-09. He was succeeded in the finance portfolio by Joe Oliver, who has kept a lower profile.
But while his presence on the campaign trail will be missed, not having his name on the ballot could make space for other Tories to step up, said Jaime Watt, executive chairman of consulting firm Navigator Ltd. and a Conservative.
He doesn't think Flaherty's absence will be felt more than any of the other missing notable Tories.
"I always think of politics as a team sport," Watt said.
"When the tall trees get chopped down, it gives some of the other trees room to grow."
He believes Oliver, a former Bay Street banker, has done a good job filling Flaherty's shoes without trying to mimic his predecessor's style.
Near the end of his cabinet career, Flaherty also showed he wasn't afraid to speak out, even if it meant questioning policy announced by his boss.
About a month before he left cabinet, he publicly questioned a controversial Tory promise to introduce income-splitting for couples with kids — a key platform pledge from the party's 2011 campaign.
Flaherty suggested there were better ways to spend billions in government surpluses, such as paying down the public debt.
Harper eventually reiterated his support for income splitting after many members of the Tory caucus insisted the government could not ditch the promise. It's unclear whether Flaherty and Harper actually quarrelled over the issue.
The Harper government eventually introduced the income-splitting plan.
Watt, however, didn't consider Flaherty a big dissenter. He couldn't think of any other differences between Harper and Flaherty that were aired publicly over the years.
"I actually think there was very little sunlight between the two of them."
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