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Ebbsfleet claimed their first home league win under new boss Dennis Kutrieb - despite playing the second half with 10 men.
Fleet trailed at the break but second-half goals from Lee Martin and the outstanding Bobby-Joe Taylor turned the game in their favour.
Hungerford took just three minutes to go ahead. Callum Willmoth's free-kick into the box was met by the unmarked Mike Jones. Fleet keeper Jordan Holmes saved the first effort but Jones made no mistake to turn home the rebound.
Fleet's response was swift, Rakish Bingham feeding Reece Grant five minutes later and he confidently slotted low beyond keeper Luke Cairney.
It was the home side who then go on top. Bobby Joe-Taylor was particularly prominent down the left, producing a couple of dangerous crosses.
Taylor set up Bingham, whose shot was turned over. The resulting corner saw Cairney fumble a low shot but Grant's blushes were spared by the offside flag as he somehow turned the ball over the bar from five yards.
Josh Payne's left-wing corner hit the top of the bar and bounced out of play before Taylor crossed for Grant, whose near-post effort hit the post.
Hungerford regained the lead against the run of play on 37 minutes when they won the ball deep in Fleet territory and Luke Hopper produced an accomplished finish.
There was a niggly undercurrent throughout the half and things boiled over in stoppage time. James Rusby was booked for taking out Grant and before the free-kick was taken, a Hungerford player went down in the box.
After consulting his assistant, referee Steven Hughes produced a red card for Fleet defender Charlie Rowan, amid vocal protests from those Fleet volunteers inside an almost-empty Stonebridge Road.
Fleet dropped Josh Payne deeper as part of a three-man defence and the 10 men dominated possession in the second half.
Taylor was again to the fore, his left-foot shot was saved before Fleet deservedly levelled on 66 minutes. Skipper Martin fired home from 20 yards to put his team back on level terms.
Both teams exchanged yellow cards as the tackles continued to fly in during a keenly-contested game - although Hungerford's Matt Partridge was fortunate to avoid a straight red card for a shocking challenge near halfway.
But there was only one team playing football and Ebbsfleet's persistence paid off with 10 minutes left when a flowing move ended with Martin crossing for the arriving Taylor to head them in front.
Hungerford's Harrison Bayley was booked for a two-footed lunge at substitute Ben Frempah in the 90th minute and while Hungerford went close through Curtis Angell's header in stoppage time, it was no less than Ebbsfleet deserved.
Ebbsfleet: Holmes, Adebayo-Rowling, Rowan, Kahraman, Taylor, Mekki (Frempah 46mins), Payne (Chapman 87mins), Paxman, Martin, Grant (West 76mins), Bingham. Subs not used: Hadler, Wood.
Hungerford: Cairney, McGrory (Taylor 83mins), Angell, Partridge, Emberson, Rusby, Jones, Willmoth (Edwards 83mins), Seager, Bayley, Hopper (Harding 71mins). Subs not used: Berry-Hargreaves, Graham.