The formal reason for the ban is Telegram's refusal to collaborate with the FSB in decrypting or tracking the messages of a purported terrorist group. (Sources: Bloomberg, court order)
Quoting Roskomnadzor (i.e. the Internet censorship department) itself:
On the basis of Art. 15.4 of Federal Law No. 149-FZ "On Information, Information Technologies and Information Protection" Roskomnadzor sent a notice to Telegram Messenger Limited about the need to fulfill the responsibilities for communication services.
In accordance with Art. 10.1 of Law No. 149-FZ, these responsibilities are to provide the federal executive body in the field of security (the FSB of Russia) with the information necessary to decode received, transmitted, delivered and (or) processed electronic messages.
The fact that Telegram Messenger Limited did not fulfill the lawful requirements was confirmed by the decision of the justice of the peace in Judicial Section No. 383 of Meshchansky District of Moscow in case No. 5-1794 / 2017 of October 16, 2017, which entered into force on December 12, 2017.
In accordance with Part 1 of Art. 15.4 of Law No. 149-FZ, the above duties must be fulfilled within 15 days from the receipt of this notice.
March 20, 2018
In other words, some "terrorists" purportedly used Telegram to exchange messages and Telegram refused to "collaborate" with the FSB in decrypting those messages. WhatsApp, on the other hand, has not been (yet) held accountable for such "recalcitrance".
The likely real reasons behind the ban have already been nicely explained in the other answer.
