Open two instances of the same PDF in Mac OS X Preview

Open a document in a new instance of its associated application like this:

open -n path/to/file.pdf

Open also allows you to specify the application for the file, but if Preview is your default PDF viewer, you don't need to.

Another option is to bookmark relevant pages of the document, and jump between them by using the Back and Forward commands (Cmd-[ and Cmd-]).

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The command above can be wrapped in a Service that can be assigned a keyboard shortcut in System Preferences » Keyboard using Automator:

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Unfortunately, Preview cannot be scripted, and this Service cannot be launched from within Preview when viewing the document. You can, however, use it in Finder, either via its Finder » Services menu, or the context-menu of any file.

Hit P or choose File > Print and when the print dialog comes up, instead of printing choose Open PDF in Preview from the PDF menu.

This will open another instance of the document without opening another instance of the Preview application, so you can switch between the two documents using ` as normal. In addition, this instance is only located in temporary memory and will not need to be deleted after closing. However, depending on your printer's settings, the resolution and margins may be affected.