When you make a transaction, you relay it to other peers. Someone connected to pretty much every peer will be able to mostly accurately tell who made a transaction, and that tells which IP owns which address.
It's possible to get around this, just proxy transactions or use blockchain.info's pushtx.
Alright, actually i wanted to know more about atlantis and silkroad's transaction system.
They are onion based sites, so you can't find ip address of their server,so i was wondering if they can get tracked by their bitcoin address/transactions or not.