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In the past, I grew some herbs which I harvest them when I see them grow out of space. Then I just cut the whole stem, then the plant will split in 2 ways growing in a Y shape. The next time it grew out of space, I cut the whole stem again, and produce another Y shape branch. Eventually its leaves become smaller and are too small to harvest.

Is this a bad way of harvest? Should I just take the leaves?

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I think the answer will depend on the herb - some herbs you eat the seeds, some the leaves, some the stems. In the case of chives (a monocot) the leaves grow like stems, etc. –  winwaed Mar 23 '12 at 12:26
    
How about basil? –  lamwaiman1988 Mar 25 '12 at 17:22
    
We pull the leaves off for cooking; but cut the stems when it bolts. Actually when it bolts we tend to let it bolt and then sprinkle the resulting seeds in the top of the pot. We get lots of basil, and then it re-seeds for the following year. –  winwaed Mar 25 '12 at 23:36

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If you're growing indoors, I'd expect to need to replant non-woody leaf herbs like basil at least once a year, if not more. For woody leaf herbs, like rosemary, you should be able to get several years.

It's hard to give specific advice without a photo. However, when you get to the point you describe, you probably need to do something drastic - a hard prune, repot, or start another.

If the plant has more than one stem, or has low branches that would "volunteer" to become a new stem, you probably occasionally want to cut back the main stem very hard when it stops being productive.

If it's in a pot, consider the possibility that the plant is root-bound - has too much root for the pot. In this case, you want to both cut it back (to reduce stress from repotting) and repot.

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