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Manigault, 53, of Hollywood is accused of breaking into Mudgett's home and killing her, Maj. Eric Watson of the Charleston County Sheriff's Office said late Friday.
Police are also "looking very hard" at Manigault in connection with the homicide Monday of Polly Ann Mitchell, 70, of Bluffton, though police have not charged him in her death, Capt. Joseph Manning of the Bluffton Police Department said.
About 5 p.m. Friday, an unidentified body was found in Hollywood. It was wrapped in a sheet or blanket in a densely wooded area about a half-mile from Mudgett's home on Toogoodoo Road, Watson said.
Investigators and a coroner planned to remain on the scene into the night, Watson said, adding the body had not been identified.
Bluffton's Manning said he was keeping in touch with Charleston detectives. "Until we get a positive ID, that it is in fact the body (of Mudgett), we'll keep searching in our jurisdiction" for her, Manning said.
Watson and Manning declined to release additional details, citing the ongoing investigations.
Detectives determined Manigault was a suspect in Mudgett's disappearance after several people phoned in tips that he had been driving Mudgett's Hyundai in Bluffton within days of her disappearance early last week, Watson said. The car was seen near Mitchell's Buck Island Road home Monday shortly before she was killed and was found submerged near a boat landing in Ridgeland later Monday afternoon, authorities say.
The Hollywood man was arrested Monday in Bluffton on a warrant for failure to re-register as a sex offender. He also was charged with cocaine possession, according to the jail log.
Manigault frequents the Buck Island Road and Simmonsville Road area in Bluffton, Manning said.
Charleston investigators said they also believe Manigault and Mudgett had met before. "We don't know how many times, but he knew of her for quite a while," Watson said.
Charleston and Bluffton investigators have tried to interview Manigault, who remained in a Charleston jail Friday, but say he has not cooperated. Bluffton officers may try to speak with him again next week, Manning said.
Charleston investigators finished testing Mudgett's vehicle and were checking the scene where the body was found for evidence, Watson said.
Since late last week, they have declined to provide details about what happened in Mudgett's house.
Watson said Thursday that investigators found Mudgett's house in disarray -- perhaps a signal that the perpetrators had not thought out the crime -- but has refused to provide further details.
Island Packet and Beaufort Gazette staff writer Zach Murdock and Andrew Knapp and Dave Munday, staff writers with The (Charleston) Post & Courier, contributed to this report.
Follow reporter Rebecca Lurye on Twitter at twitter.com/IPBG_Rebecca.