Mersin İdmanyurdu took place in Group 1 in 1999–2000 Second League season. League was played in three stages. In the first stage, 50 teams in five groups (10 clubs in each) played for the first two rankings to play in the promotion group. The promotion group consisted of those 10 teams. At the end of the second stage top two teams promoted to 2000–01 First League. The remaining 8 teams in each ranking group played in classification groups, by carrying points and goals from ranking groups. Bottom two teams in Groups 2, 4, 5 relegated to 2000–01 Third League at the end of the season. Due to the earthquake that occurred on August 17, 1999, Sakaryaspor and Düzcespor in Group 1 and Darıca Gençlerbirliği in Group 3 withdrew from the league and demanded excuse. TFF has decided that the teams would not be relegated. One another worst team from Group 1 and two other worst teams in Group 3 had relegated at the end of the season. In the third stage, 8 clubs (3 from the promotion group and 1 each from 5 classification groups) played one-leg play-off games in Antalya Atatürk Stadium to determine the third team to be promoted to First League.