I don't see anything in their trademark policy that implies they have registered any of their marks yet. In fact, all the marks in the "included, but not limited to" list use ™ instead of ®, the later which can only be used with registered trademarks. Searching the USPTO database[1] for "let's encrypt" only reveals Comodo's 1B registrations.

All that being said, under US law you still have trademark rights even before you register the mark, and ISRG definitely has first use on the Let's Encrypt mark.

[1] http://tmsearch.uspto.gov/bin/gate.exe?f=login&p_lang=englis...