The Wire star scores a nomination from the British Academy of Film and Television Arts (BAFTA) for his role in Luther, while Whishaw is in the frame for the prize for thriller London Spy. They will face stiff competition from Oscar winner Mark Rylance, who is nominated for Wolf Hall, and Stephen Graham for This Is England '90.
Rylance's co-star Claire Foy also earns a nod for Wolf Hall, which leads with four nominations. Foy competes against Sheridan Smith for The C Word, Suranne Jones for Doctor Foster and Ruth Madeley for Don't Take My Baby.
Wolf Hall also leads the Drama Series category, and will have to do battle with sci-fi thriller Humans, The Last Panthers and No Offence, while Whishaw's London Spy lands a mention in the Mini-Series shortlist with Doctor Foster, This Is England '90 and Timothy Spall's horror The Enfield Haunting. Nominees for the International series prize include The Good Wife, Spiral, Narcos and Transparent.
Veteran actors Ian MCKellen and Tom Courtenay will compete for the Supporting Actor trophy for The Dresser and Unforgiven respectively, while Lesley Manville and Michelle Gomez score Supporting Actress mentions for River and Doctor Who respectively.
Downton Abbey star Hugh Bonneville scores a Male Performance in a Comedy Programme nomination for W1A and will go up against Toby Jones for Detectorists, Javone Prince for his self-titled show and Peter Kay for Peter Kay's Car Share.
Spy actress Miranda Hart is in competition for the female comedy equivalent for Miranda, while Sharon Horgan is nominated for Catastrophe, Sian Gibson for Peter Kay's Car Share and Michaela Coel for Chewing Gum.
Adele also lands a nod for her TV special Adele at the BBC, and will compete with Britain's Got Talent, Strictly Come Dancing and TGI Friday's anniversary special for Entertainment Programme. Stephen Fry also earns a mention for Entertainment Performance for long-running panel show QI.
The winners will be announced at London's Royal Festival Hall on 8 May (16).