 In 1998, Markarian coached the Greek team, Ionikos, reaching fifth place in the Greek league and qualifying them for the UEFA Cup.Markarian became the coach of the Paraguay National team from 1999 through 2001 qualifying Paraguay to the 2002 World Cup in Korea and Japan.He was fired by the Paraguayan Football Association in 2001 prior to the World Cup because he had lost his last two qualifier matches, a 3-1 away loss against Venezuela and a 0-4 home loss against Colombia.