 <p>In the project's properties (right-click on project => Properties => Resource) there is a Text File Encoding section.</p> <p>Did you configure the encoding here? If not, you have two choices : "Inherited from container" (which should be the workspace default, in your case UTF-8) and "Other" which let you choose a specific encoding (ISO-88591)...</p> <p>I just tested that on one of my projects, closed it and reopened it and the ISO88591 encoding is still configured.</p> <p><em>Note that I'm using a plain Eclipse though, not a PDT project. PDT may handle encoding settings differently, but somehow I doubt that (file encoding being a low level functionality it makes sense that all plugins share this behavior).</em></p>