Little went right for Lowestoft Town as they dropped valuable home points and finished the game with just nine men.
New boss Dale Brooks will be without Jake Reed and Travis Cole after both saw red.
Brooks included loan signing Matty Foy, from Cambridge United, in the starting line up, but was without the suspended Jacek Zielonka.
There was a sign of things to come as early as the seventh minute with Kane Haysman's low cross flicked goalwards by Jordan Chiedozie, but saved by Ben Dudzinski.
However, Lowestoft were creating the better chances, with Callum White feeding Reed, who pushed his effort wide. The same pair combined again and from the full-back's cross Foy was just wide of the upright. The best chance fell to Sam Borrer from Andrew Fisk's shrewd pass, but Lennie Pidgeley was off his line quickly to save.
Margate went ahead on 38 minute, somewhat against the run of play – White was caught in possession deep in his own area and in the scramble that following Haysman prodded the ball home.
In the second period Fisk again split the Margate defence, picking out Reed whose shot flashed just wide of the target. Haysman headed over for the visitors, while at the other end Adam Smith was narrowly wide from a direct free-kick and Foy's rising drive was pushed over the bar.
But Town's hopes suffered a blow on 68 minutes when Reed was sent off – having been fouled he petulantly threw the ball into the face of his opponent.
And any slim hopes disappeared in the 77th minute when Cole followed, having brought down Jordan Chiedozie in the area with the big striker getting up to convert the spot-kick.
Despite the defeat, Brooks will take heart from a performance which showed a lot of character whilst getting little in the way of good fortune.
Lowestoft: Dudzinski, White, Smith, Cole, Barker, McAuley, Fisk, Jarvis (Bammant 73), Reed, Foy (Greenleaf 80), Borrer, Subs not used: Hodd, Wren.
Margate: Pidgeley, Bodkin (Wynter 72), Mills, Rogers, Friend, Swift, Haysman, Prescott, Chiedozie (Enver-Marum 80), Collin, May (Martin 72), Subs not used: Brown, Stannard.
Ref: G Laflin. Attendance: 358
Comments: Our rules
We want our comments to be a lively and valuable part of our community - a place where readers can debate and engage with the most important local issues. The ability to comment on our stories is a privilege, not a right, however, and that privilege may be withdrawn if it is abused or misused.
Please report any comments that break our rules.
Read the rules here