If you hold your shares in a brokerage account and don’t specify a method when you sell your shares, this is the default method that determines the shares you used. With the first in, first out method, the shares you’re selling are the first ones you bought.
In most cases, selling shares in the order in which you bought them gives you the bigger gain because the market usually goes up over time. If you’ve held the shares for various lengths of time, selling the ones that you bought first can mean the difference between getting the favorable long-term capital gains rate or not.
If you want to sell other shares, you must specifically identify those shares in writing prior to the sale and receive a confirmation from the broker that those shares will be sold.