The award also included a grant of £334,000 to help develop the project to the next stage.
The centre is set to be completely refurbished.
As well as opening the existing collections and creating a new tourist attraction, the aim is to turn the museum into a centre for research supporting community regeneration and international development.
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The Chair of the David Livingstone Trust, Dr Isabel Bruce, said: "There is a lot of hard work ahead, but the generous support we have received from HLF, as well as the help from the National Trust for Scotland, South Lanarkshire Council and others, allows us to move forward purposefully to realise our ambitions for the Centre."
Provost Eileen Logan said: "As South Lanarkshire’s Provost and a Trustee of the David Livingstone Trust I am doubly delighted that HLF has handed us a tremendous boost to the long-term plans for this iconic internationally important facility."
Head of HLF Scotland, Colin McLean, said: "We are delighted to give our initial support to a project which will allow us to celebrate this rich heritage and put David Livingstone’s birthplace on the world’s stage as a tourist destination and valuable education resource."
(LM)
