Connor Gibson, 19, appeared at Hamilton Sheriff Court on Friday accused of murder, sexual assault by penetration and an attempt to pervert the course of justice.
He made no plea and was remanded in custody pending a further court appearance.
Amber, 16, left her home in the Hillhouse area of Hamilton, South Lanarkshire, at about 9.15pm last Friday and was reported missing later that night.
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Her body was discovered in the town's Cadzow Glen park at about 10.10am on Sunday.
A police watchdog has been ordered to investigate Police Scotland's handling of the case, understood to relate to the missing person investigation.
A spokesman said: "The Crown Office and Procurator Fiscal Service has instructed the Police Investigations and Review Commissioner to investigate the circumstances leading up to the death of a 16 year-old girl in Hamilton."