By default, tooltips are drawn using the old UI system, so it is located on top of the uGUI elements.
To work around this, draw the tooltips using uGUI.
Example:
http://infinity-code.com/atlas/online-m … ample.html

I use "Online Maps" to put some 3D markers on the map. Sometimes i need to show tooltips (it may be one or more at one moment) for placed markers (1 tooltip for 1 marker of course).

The problem is that when i need to show some popup (not GUI), tooltips always show over popup, not behind it.

There is the code i use to my needs:

....
marker3D.OnDrawTooltip += onCustomMarkerDrawTooltip;
....

void onCustomMarkerDrawTooltip(OnlineMapsMarkerBase marker){

    OnlineMapsMarker3D tmpMarker = marker as OnlineMapsMarker3D;
    Vector2 screenPosition = OnlineMapsControlBase.instance.GetScreenPosition(tmpMarker.position);
    GUIContent tip = new GUIContent(tmpMarker.label);
    Vector2 size = tooltipStyle.CalcSize(tip);
    GUI.Label(new Rect(screenPosition.x - size.x / 2 - 5, Screen.height - screenPosition.y - size.y - 20, size.x + 10, size.y + 5), tmpMarker.label, tooltipStyle);

}

Maybe somebody knows how to put tooltips behind the objects? Thank you!