This reservation can't be booked online.

You may be able to book a reservation from Trakiszki on the PKP IC website - domestic reservations are normally possible there. Otherwise at any Polish ticket office or (probably) in Lithuania.

If you are before in Germany, you should be able to book it at a ticket office there.

Otherwise also some rail agents might be able to book it.

Via DB the reservation is 4,5€, directly via LTG it is 5€ (as some agents do).

Reserved seat will be on both trains the same.

according to some reports this connection is used quite well now. In September when I used the „old one“ it was almost empty.

In Lithuania seat reservation is possible only in train or ticket office, it costs €5 and valid for all route, for example Vilnius-Krakow.

The main problem is that different companies (Lithuanian and Polish) appointed a limited number of seats for international passengers in their trains (about 90 in total) and sometimes all tickets are sold a few days before the journey.
But the real number of train seats is larger and used for local transfers. So one of the options would be to buy a seat reservation for a Lithuanian train from Vilnius to Mockava and Polish from Trakiszki to Warsaw/Krakow. Tickets are always available on the same day

Am I correct in thinking that a seat reservation is not mandatory in the train between Vilnius and Mockava?

Officially it is mandatory (seat reservations - required) in Vilnius-Mockava train, but the staff often allows you to travel without it. On the other hand, all seats are numbered and you just will need to stand sometimes.

Thanks for your input. 

I did ask Polrail for a quote for this traject: they could offer the reservation (already before 30 days before travelogue) but charged over 10EUR a person which I think was relatively expensive compare to normal price ticket.

So I took the chance to wait until we are in Vilnius. 

But not a complete 100% gamble: I made an online reservation for the Polish part of the traject (Trakiszki to Krakau which cost 1 zlty per seat). 

So for the Lithuanian part we will see what will happen. 

I'm also planning to travel the same route this summer. 

Could you please elaborate on how it went? Was it possible to reserve a seat from Vilnus to Moscava on the spot?

Also, I see that you still managed to book an online reservation from Trakiszki to Krakau. But I am confused what happens between Moscava and Trakiszki..

I would be very thankful to hear how the journey went.

• @rvdborgt - I haven’t asked explicitly but I do think for the part Vilnius- Mockava a seat reservation is mandatory. We went to the train station the day before we had to take the train and paid EUR 5 per person for the seat reservation. The lady was very kind and made a print (instead of the normal receipt for domestic travel) of the reservation. In the train we were asked to show it. And the way they asked, I think if we hadn’t one, they would have made a problem of it. 
• Make sure you write down the destination - the lady heard Warsaw instead of Krakow (due to my prononcation I guess;.) ) so we had the reservation to W. But because I also had the reservation for the Polish part, this wasn’t a problem for us. 
• We had a 1st class pass - but the train Vilnius - Mockava has only 2nd class (and is quite a cramped seating, little space for big luggage but friendly personal - they came to explain the delay in person. ) And for the part M-Poland you have a reservation but no seat number. So from that perspective it is worth to pay the 1 zlt and make the seat reservation for the polish part. 
• @cipis - Between Mockava and Trakiszki is a little bit grey area. Because we had a seat reservation for T to Krakow in 1st class, we already sit there from M onwards. The conductor was wondering if this was ok (how did we got a seat there since it was not possible to book online for that part) , but he checked our ticket in the interrail app and for him this was ok. 
• I hope this will help you and have a nice trip. 

Thank you so much for the previous answers! I really appreciate the quick response! Really cleared things up for me.

But I am wondering about this part. Did you mention your destination to the Lithuanian ticket office (Krakow), even if you had already reserved the seats online (Trakiszki to Krakow)?

Because I now understand that you have to reserve the seats from Vilnus to Mockava in person and Polish train route part online, yes? And show both my pass QR code to the train conductor and the specific seat reservations (in both Lithuania and Poland)?

Excuse my confusion, this is my first time

interrailing and the app hasn't been any help to me for this specific train route

I have a similar problem. I want to travel from Vilnius to Krakow tomorrow and just went to the train station. All trains for the next days are sold out. It's however still possible to purchase a regular ticket on the PKP website. I also made a seat a reservation for Trakiszki-Krakow and I pray I won't get fined or kicked out

I'm also planning to take this route.

Did everything goes well ?