The issue was that in the past JDK (offered by Sun and Oracle) had no binaries available for FreeBSD (I believe the source was available but was not the same that Sun JDK was built from). If you wanted to run it, you would have to download the Linux version and run it in compatibility mode.

Later FreeBSD get some kind of deal with Sun to provide native Sun JDK for FreeBSD and made them available through http://www.freebsd.org (you can check web archive to see older versions).

Nowadays starting since JDK 7, OpenJDK supposed to be fully compatible with OracleJDK, so it should no longer be a problem anymore.