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In our first year on the farm, we planted fruit trees and went to a lot of trouble to buy markers and write on each one of them. We had the variety and date it was planted. Luckily we also wrote all the information in a spreadsheet! The ink from regular Sharpie markers lasted less than two months.
We then got smarter and purchased oil based markers. These really work! They stay on all summer. I still don’t trust the ink for long term but at least you can get through the season. They work for quite a while too if you take care of them. (Don’t leave them in your coveralls to freeze all winter…)
We also searched for different garden markers. We have purchased some off ebay, off Amazon, and a variety of local stores (in which you typically can’t get good prices as they don’t sell in bulk). In the end, we found the ones at Lee Valley were the best. They come in a variety pack of colours and are LARGE enough to see! These ones were used all summer. They are still in great condition and will be reused next year. We try to colour code varieties or different species. Here’s the link to Lee Valley: http://www.leevalley.com/en/garden/page.aspx?p=71761&cat=2,43319,33281