Template:1998–99 Conference USA men's basketball standings


 * colspan="15" style="text-align:center;background-color:#CCCCCC;color:black;" | American
 * colspan="15" style="text-align:center;background-color:#CCCCCC;color:black;" | American


 * colspan="15" style="text-align:center;background-color:#CCCCCC;color:black;" | National
 * colspan="15" style="text-align:center;background-color:#CCCCCC;color:black;" | National