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The leaves with the lines areThe leaves with the lines are the first two "true leaves". The flat leaves below them are called seed leaves, these will fall off soon on their own. Do not pinch your basil just yet, they will be stunted as their first true leaves are important. According to the instructions, "After the seedlings have their first six leaves, prune to above the second set." This means you should start pinching your basil only after they have 6 leaves with lines. Then only prune 2 leaves off. From that spot, two new branches will appear with two leaves of their own. You should only prune 1/3 of the plant at a time.

2015 Special Edition Garden GuideCooking Fresh with The Old Farmer's AlmanacThe Almanac Monthly Digital MagazineWhat the heck is a Garden Hod?