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I grouped the layers in ArcGIS Desktop and published them to my Portal for ArcGIS, but when I tried to create the Map Application, I see the individual layers. They are not in a group.

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Portal does not support grouped layers. You can only have grouped layers if you share as a web service and include the service in your web map.

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I agree with Zara. Unfortunately, Portal doesn't support group layer as of 10.6. A workaround that I have been using is to group the layers in .mxd and publish them as one service. Then I would add these service in the Portal's WebMap. One caveat to this process is, any time you make non-trivial changes in one of the layer, you will have to republish the whole service and add the new REST URL in Webmap again. Then you might have to reconfigure all of your formattings in the service (like pop-ups).

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