The root certificate is the starting point of a chain of trust upon which an SSL certificate is issued. The root certificate belongs to the Certificate Authority. The root certificate is used to issue intermediate certificates, that in term make it possible to register SSL certificates for end users. These certificates inherit the trust level from the root certificate.
Each browser or service that makes use of SSL certificates contains a list of approved root certificates. Whenever a website is visited over an SSL connection, the validity of the certificate is checked by verifying the fingerprints of the certificate and the accompanying intermediate certificate, until the fingerprint of the root has been reached. This is then checked against the root certificate in the browser. If these do not match, the certificate will not be valid.