I'm also puzzled that Let's Encrypt's Trademark policy [1] strongly suggests that 'Let's Encrypt' is a trademark (word mark?) that they have registered, and yet according to the most recent letter sent by the USPTO [2] "The Office records have been searched and there are no similar registered or pending marks that would bar registration [...]"
You don't have to register trademarks, even though it's a good idea to do so, if only for the sake of clarity. Trademarks can be established through market use (common law usage), which is what Let's Encrypt's claim is based on.
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.
This seems like a good example of why you should go through the registration though. Because now they are going to have to use the courts to resolve the situation; presumably (I hope?), if they'd registered, a new registration application for the exact same mark would not even be accepted.
There's a challenge period during trademark registration when they can voice their objections. They may be able block it if they're not too late.
> You may challenge an application for trademark registration at the USPTO by filing an opposition with the TTAB within 30 days after it is published in the Official Gazette.
Ah, ok. I hadn't realised there was a difference between registering a trademark and just publicly claiming it as your own. That helps to clear up what the situation is here.
[1] https://letsencrypt.org/trademarks/ [2] http://tsdr.uspto.gov/documentviewer?caseId=sn86790719&docId...