This is something that shouldn’t be of concern to most of you yet as a lot of ISPs haven’t yet made the jump to IPv6 connections for websites.
The difference between the two is that IPv4 connections consist of 4 groups of 3 digits. Such as your regular IP address a la 126.96.36.199 which is your standard IP address. IPv6 addresses have a much different configuration consisting of letters and numbers. Although with IPv6 addresses if you have more than four zeros in a row you can omit them.
So, in theory if you did have an IPv6 address, you have two versions of your site on two different connections. Which usually would account to duplicate content. Thankfully Google has devised a way to tell whether the same site is on a different connection rather than a different host/domain (which would be a duplicate content issue).
Matt Cutts explains it all here:
Blog Post by: Greg McVey