Gemma McCluskie's headless and limbless body was discovered floating in the Regent's Canal in Hackney, east London, last week.
She had been missing for a week after attending the opening of the new £650 million Royal London Hospital in Whitechapel, east London.
The 29-year-old was last seen returning to the home in Pelter Street, Hackney, that she shared with her brother, Tony.
No bail application was made when McCluskie, 35, appeared in court by video-link from Brixton Prison.
He was remanded to a plea and case management hearing on June 18 following the brief appearance.
No other members of the family were in court.
Miss McCluskie played Kerry Skinner in the BBC soap in 2001.
Friends launched extensive searches across east London in a bid to find her and former EastEnders co-stars Natalie Cassidy and Brooke Kinsella both appealed on Twitter for help.