Default is FIFO. You would probably want to sell 30k from the first 100k that at that time will qualify for long term capital gains, thus FIFO. I'm not with E trade, but TDA does track for you - and I would assume E trade would as well. All of this, of course, is assuming you are trading a US "taxable" account (not IRA, etc). Also beware that you will be responsible for taxes on all gains in the quarter that you sell (can't wait until year end without penalty). I hope you make a killing!