I'm going to answer my own question here.

It turns out that akka-cluster-sharding registers its own serializer which 
is based on protobuf. It's a bit hard to find because it's all private but 
here is it on 
Github: 
https://github.com/akka/akka/blob/master/akka-cluster-sharding/src/main/scala/akka/cluster/sharding/protobuf/ClusterShardingMessageSerializer.scala

I used this test to find out what the serializer 
is: https://gist.github.com/leonardehrenfried/99194ad1164049434d187a5b4068b008

On Tuesday, November 15, 2016 at 10:37:31 AM UTC+1, Leonard Ehrenfried 
wrote:
>
> Hello,
>
> we do event sourcing with akka-persistence and akka-cluster-sharding. 
> Apart from our own messages/events akka-cluster also writes a few messages 
> regarding shard allocation to our event log.
>
> We have configured a custom serializer for our own events which transforms 
> them to JSON but which format is chosen by default for the cluster messages 
> (we haven't added a configuration setting for events that aren't our own)?
>
> Is it protobuf oder java serialization? Or neither?
>
> Thanks for your help,
> Leonard
>

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