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When I try to buy something using bitcoins, how does that merchant know that I have payed them the agreed amount.
In other words, how does the merchant know that I payed for the product, and that they can start shipping the product to me. I thought that bitcoin was anonymous in its transactions
Actually, Bitcoin is pseudonymous (you interact with the network through your addresses, which are observable). At any point where anyone else gains knowledge of your ownership of an address, you potentially become identifiable. E.g. when you trade fiat for bitcoin or when you use bitcoin to buy thing online that will be sent to your address. – Murch – 2013-10-17T14:02:57.377