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I'm using a dynamic map service layer that is shown in a semi transparent way overlaid on a tiled map service.

There are a few polygon layers in the dynamic map service layer that cover the whole mapped area in different solid colors. Those layers are set as transparent in the MXD, but when the map is served out from ArcGIS server, it displays differently from in ArcMap. The layers blend down with the background MXD itself, making them turn %50 white, and making the basemap behind them as difficult to read as if they were solid.

Is there a way to serve features of mixed transparency levels from an arcgis server service?

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Is there a way to serve features of mixed transparency levels from an arcgis server service?

Yes. Please read this whitepaper from Esri:
Work with transparencies in an ArcGIS Server Web mapping application

From your description, I believe you should:

  • Analyze the map using Map Service Publishing tools.
  • Convert layer transparency to color transparency.
  • Publish to ArcGIS server as a MSD.

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