Officers looking into the background of Mark Bridger, 46, discovered that he had fathered two children with a woman called Elaine Griffiths, the Telegraph reports.
Mr Bridger and Elaine had Connor and Sophie in the 1990s. Around the same time, Elaine's sister Karen had two daughters - Hazel and Abby - with April's father Paul Jones.
He subsequently married April's mother, Coral. The connection means that Mr Bridger's children are cousins to April's half sisters.
Abby, Hazel, Connor and Sophie all took part in the search for the little girl who went missing last Monday evening from close to her home in Machynlleth, Mid Wales.
Hazel and Abby wrote on Facebook about their 'little sister' and also released a pink balloon in hope for her safe return.
Their mother Karen said: "The past week has been very hard and the community support for the family has been overwhelming.
"We are trying to focus all our energy on finding little April and staying strong for all the family members involved."
Mr Bridger, a former lifeguard and abattoir worker, has been charged with April's murder as well as child abduction and unlawfully disposing of and concealing her body with intent to pervert the course of justice.
Police have said they are continuing an intensive search for April but fear she may never be found, with speculation that her body may have been washed out to sea.