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SNP leader and Scottish First Minister Alex Salmond congratulated Mr McDonald on a "fantastic SNP win", adding he would be a "first-class representative for the people of Donside".
The by-election was held following the death in April of Nationalist MSP Brian Adam, who had been suffering from cancer.
Mark McDonald said that by winning the seat he had "protected the legacy of the late Brian Adam, who was a great mentor to me and a great friend of mine".
He added: "We worked hard, we put up a good campaign on the issues that mattered to the people of Aberdeen Donside. We wanted to make sure we protected the legacy of Brian Adam.
"Our objective was to win the seat, now we've won the seat the hard work starts."
The Scottish National Party has won the Aberdeen Donside by-election, but with a greatly reduced majority.
Mark McDonald won the seat after polling 9,814 votes, just over 2,000 more than the Labour candidate who was his nearest rival in the contest.
However the SNP's majority fell by more than 5,000 votes from the result in the 2011 Scottish Parliament election.
- Mark McDonald (SNP) 9,814
- Willie Young (Labour) 7,789
- Christine Jardine (Liberal Democrat) 1,940
- Ross Thomson (Conservative) 1,791
- Otto Inglis (UKIP) 1,128
The Scottish National Party has held Aberdeen Donside in the by-election, with Mark McDonald elected as the MSP for the constituency.