These are the works I have referred to in compiling the story of Bothwell's life. I hope to be able to reference more fully eventually, and add sources regularly, so keep checking back.
Calendar of State Papers Domestic 1547-1580. Edward VI, Mary and Elizabeth. ed R Lemon. (Longman, Brown, Green, Longmans and Roberts, 1856)
Calendar of State Papers relating to English Affairs (Rome) Ed J. M. Rigg (1916)
Calendar of Letters and State Papers relating to English Affairs, preserved principally in the Archives of Simancas. Vol I, Elizabeth 1558-1567. Ed Martin AS Hume (PRO 1892)
Calendar of State Papers, Foreign Series, of the reign of Elizabeth (vol VIII 1566-68). Ed Allan James Crosby (Longman and Co, 1871)
Calendar of State Papers, Foreign Series, of the Reign of Elizabeth I, 1558-89 (23 Vols). Ed Joseph Stevenson, WB Turnbull et al (London, 1863-1950)
Calendar of State Papers relating to Scotland and Mary Queen of Scots Vols I and II. Ed Joseph Bain (HM General Register House, Edinburgh, 1898, 1900)
Calendar of State Papers Venetian, 1558-1580. Ed. Rawdon Brown and G Cavendish Bentinck (HMSO, 1890)
SP/12/207. Public Record Office
SP/52/13. Public Record Office
Register of the Privy Council of Scotland Vol I, 1545-1569. ed J Hill Burton. (Register House, Edinburgh)
Records of the Burgh of Edinburgh
Armstrong Davison MH; The Casket Letters; A solution to the Mystery of Mary Queen of Scots and the Murder of Lord Darnley. (Washington DC University Press USA, 1965)
Bax C (ed); The Silver Casket: Being Love-Letters and Love-Poems attributed to Mary Stuart, Queen of Scots, now modernised and translated, with an Introduction. (Hume and van Thal Ltd, 1946)
Bingham C; Darnley. A Life of Henry Stuart Lord Darnley, Consort of Mary Queen of Scots.(Constable and Co Ltd, 1995)
Blackwood A; ‘History of Mary Queen of Scots: A fragment’(Maitland Club, Edinburgh 1834)
Buchanan G; ‘The Tyrannous Reign of Mary Stewart’. Trans/ed WA Gatherer. (Edinburgh University Press 1958).
Camden W; ‘Annales Rerum Anglicarum et Hibernicarum Regnante Elizabetha. Trans T Hearne.
Donaldson G; The First Trial of Mary Queen of Scots (Batsford , 1969)
Drummond H; ‘The Queen’s Man’ . Frewin
Fraser A; ‘Mary Queen of Scots’. (Mandarin 1989)
Gore-Brown R; ‘Lord Bothwell’. (Collins, 1937)
Hay Fleming D; ‘Mary Queen of Scots from her birth till her flight into England’. (Hodder and Stoughton, 1898).
Henderson TF; Mary Queen of Scots: Her environment and Tragedy. Vol II (Hutchinson 1905)
Hepburn J, Earl of Bothwell; ‘Les Affaires du Conte de Boduel’. (Bannatyne Club, Edinburgh, 1829)
Hepburn J, Earl of Bothwell; ‘Confession’.
Hume MAS; 'The Love Affairs of Mary Queen of Scots'. (Eveleigh Nash, London, 1903)
Keith R; ‘History of the Affairs of Church and State in Scotland down to 1567’. Ed JP Lawson. (Spottiswoode Society 1844-50)
Knox J; ‘History of the Reformation of Religion in Scotland’. Revised and ed Cuthbert Lennox. (Andrew Melrose, 1905)
Labanoff AI; ‘Lettres et Memoirs de Marie, Reine d’Ecosse’.
Lang A; ‘The Mystery of Mary Stuart’. (Longmans, Green and Co, 1901)
Lindsay of Pitscottie; ‘Chronicles of Scotland’
Mahon RH; ‘Mary Queen of Scots: A study of the Lennox Narrative’. (Cambridge University Press, 1930)
Mahon RH; ‘The Tragedy of Kirk o’ Field’.(Cambridge University Press, 1930)
Maxwell J, Baron Herries; ‘Historical Memoirs of the Reign of Mary Queen of Scots’. ed R Pitcairn (Abbotsford Club, 1836)
Melville Sir J of Halhill; ‘Memoirs of his own life’. Ed T Thomson. (Bannatyne Club Edinburgh 1827)
Mumby FA; The Fall of Mary Stuart: A Narrative in Contemporary Letters (Constable, 1921)
Nau C; ‘The History of Mary Stewart, from the Murder of Riccio until her flight into England’. ed and intro. Revd J Stevenson. (William Paterson, 1883)
Pearson K; ‘Skull and Portraits of Henry Stuart, Lord Darnley, and their bearing on the Tragedy of Mary Queen of Scots’. Biometrika XX, July 1928.
Pitcairn R (ed); ‘Criminal Trials in Scotland, from AD 1488 to AD 1624’. Vol I . (Bannatyne Club, Edinburgh, 1833)
Robertson J (ed); ‘The Inventories of Mary Queen of Scots’. (Bannatyne Club, 1863)
Teulet A; ‘Papiers d’Etat Relatifs a la Histoire de l’Ecosse au 16e Siecle’. (Bannatyne Club Edinburgh 1852-60)
Thomson T (Ed); A Diurnal of Remarkable Occurents that have passed within the Country of Scotland since the Death of King James the Fourth til the Year MDLXXV, from a Manuscript of the Sixteenth Century in the Possession of Sir John Maxwell og Pollock, Baronet. (Bannatyne Club, XLV, Edinburgh 1833)