The charge relates to the disappearance of Ellia Arathoon, 29.
Craig Andrew Proctor, 39, of Shephard Close, Ellesmere Port, has been remanded in police custody and is set to appear at Chester Magistrates Court tomorrow (Friday).
A 37-year-old man who was also arrested in relation to the investigation has been released on police bail pending further enquiries.
Ellia, who is from the town centre, has not been seen since Friday (October 28).
She was last spotted in the Cromwell Road and Shephard Close areas of Ellesmere Port.
Earlier today police revealed officers had discovered what are believed to be human remains close to the M53.
And tonight activity appears to be focused on an area opposite the end of Cromwell Road, alongside the motorway, close to where it crosses over the canal.
A white tent has also been erected in front of a property in Shephard Close where an officer in a police car is guarding the scene.