Vladislav Ivanchenko said he had decided to end his career immediately after receiving an anonymous text message on his way to a match between Rapid and league leaders Dacia Chisinau.
"I was told that if I don't follow certain decision in that match something could happen to my family," the 42-year-old told local television in an interview.
"It was a clear threat to my family so I decided to stop right away. I've already informed the national federation about my decision," said Ivanchenko, who was banned for two games for poor officiating by the Moldova FA (FMF) last year.
FIFA referee Gennady Sidorenko, who officiated Saturday's match between champions Sheriff Tiraspol and perennial title contenders Zimbru Chisinau, also quit after receiving a similar threat against his family. Sidorenko, 38, said he had warned his wife and daughter against going outside their house.
All four clubs have denied any wrongdoing but police and FMF officials said they have started an investigation.
Dacia, coached by former Soviet striker Igor Dobrovolsky, lead Sheriff, who have won the last 10 domestic titles, by four points with six matches left.
It was the latest in a series of incidents that have marred Moldova's most popular sport in recent years.
Club bosses often complain of poor officiating while referees say they are always under pressure from the clubs.
