I found my problem. It seems it is not enough to have the other project (MyNamespace) referenced in Presentation. Doing this let me use classes in MyNamespace in codebehind files, but not in aspx files.
I added following lines to my Web.Config file, in order to use those classes in aspx pages:
<configuration>
....
<system.web>
....
<compilation debug="true" targetFramework="4.5">
....
<assemblies>
.....
<add assembly="MyNamespace, Version=1.0.0.0, Culture=neutral, PublicKeyToke=null" />
</assemblies>
</compilation>
....
<pages>
....
<namespaces>
....
<add namespace="MyNamespace" />
</namespaces>
</pages>
</system.web>
</configuration>