I use this German-English dictionary from Babylon. It puts die in front of the German word Jahrtausend from which I infer the word is feminine, but it is neuter in other dictionaries.
Is there any reason/explanation for that?
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German compound words take the gender of the rightmost word in the meaning in which is was used to create the compound, e.g. der Elternteil vs. das Fertigteil.
German has two genders for the word "Tausend", depending on the meaning. If an entity consisting of thousand smaller entities is meant, it's neuter.
If we, however, relate to the "number 2000", Tausend becomes feminine. Usage examples:
Trotz heißer Temperaturen kamen am Wochenende an die 1000 Besucher zum Klimaschutz-Aktionstag des Kreises in Bistensee. (note the article doesn't belong to Besucher but to the "1000")
Insgesamt sollen an die 1000 Gefangene freigelassen werden
"Ich habe eine 1 in Mathe bekommen!"
Low budget free online dictionaries seem to employ scripts for gender tagging, in this case based on the "basis" word. As the basis word has two genders, the script appears to have taken on the feminine version of the word with the meaning "number 2000" and applied it to the compound.
On a side note, as for the usage of the said dictionary, I would recommend using the most authoritative sources such as Duden, DWDS or Collins Cobuild/Oxford, who have both the resources to avoid such mistakes and the renowned reputation to care about. Also refer to the list https://german.stackexchange.com/a/9535/9739 (apart from Leo, which sometimes would have weird mistakes confusing people and forcing them to ask on stack exchange, and is in general not quite informative, as it does not cite any usage cases for your enter link description here in question).