Margaret Lindsay Huggins was part of a family of four. She had a brother, Robert Douglas. Her parents were John Murray and Helen Lindsay. Her father was a solicitor, who attended Edinburgh Academy. Margaret's younger brother by three years,
Robert Douglas, attended Edinburgh Academy at the age of twelve, and then attended further education in Trinity College, Dublin in his later years. The family home was a Georgian style townhouse, at 23 Longford Terrace in Kingstown (present-day Dún Laoghaire).
Margaret's grandfather, Robert Murray, was a very important figure in her life. He was a wealthy officer at the Bank of Ireland but also enjoyed the hobby of astronomy. From a young age Margaret had a keen interest in astronomy as a result of the relationship between herself and her grandfather. When she was a young girl her grandfather brought her outdoors in the evening, and taught her about all the constellations and how they can be identified. This inspired her to be an astronomer, and she therefore attended private school in Brighton from a young age.