Yes, you can highlight text in iBooks with the Apple Pencil. This only works with an iBook, not PDFs. To use your Apple Pencil as a highlighter just find the passage of text you want to highlight and place your Pencil where you want to begin. Drag your Pencil across the text you want to highlight and you're done. To change the color of any highlighted text, or to underline any highlighted text, just tap the highlighted area and tap the color icon or red underline option when they pop up.
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