The suspect took on the identity of a fictitious Clark Rockefeller. However, his real name is Christian Karl Gerhartsreiter.
Gerhartsreiter is accused of murdering his San Marino landlord, Jonathan Sohus, 25 years ago. Sohus, along with his wife Linda, disappeared in 1985.
Gerhartsreiter left town soon after they vanished. Sohus' body was found 10 years later, his wife is still missing.
Prosecutors did not bring charges against Gerhartsreiter until March, after he had been convicted in a Massachusetts kidnapping case of his 7-year-old daughter.
Gerhartsreiter pleaded not guilty to the charges Friday. Outside court, Gerhartsreiter's Boston lawyer, Jeffrey Denner, acknowledged it was unusual to have charges brought after such a long time, but said "old case, new case, he didn't do it."
The judge ordered Gerhartsreiter to return to court Aug. 16 for a preliminary hearing. He is being held without bail.
The Associated Press contributed to this report.