Can't ssh into server if using proper domain name

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http://serverfault.com – I'm trying to login to a Ubuntu box hosted on AWS EC2, which has a route53 domain setup. The domain is resolved to the proper IP, e.g. host myhost.com and host ec2-x-x-x-x.eu-west-1.compute.amazonaws.com give the same output. I'm able to login using the amazon address like ssh -i mykey.pem [email protected], but when I try to ssh -i mykey.pem [email protected], I get Permission denied (publickey). Why can this happen? (HowTos)