See this post and I highlight the key para… http://forum.mikrotik.com/t/using-routeros-to-vlan-your-network/126489/1
Native, Base, & MGMT (management) VLAN:
As you create your VLANs and pick VLAN IDs for each one, understand that the base network that you used to initiate your first connection to a router or switch is often termed the Native VLAN. In our examples, we do not use this default network. Instead we implement a Base VLAN (our name for the management VLAN) with an ID of 99. Over this network will be device to device traffic (routing, etc.). We also default Winbox availability here as well.
A word of caution if you are thinking of using VLAN 1 in your network design. Most vendors use VLAN 1 as the native VLAN for their hardware. MikroTik uses VLAN 0. If you try to create a VLAN 1 scenario with MikroTik, and expecting tagged frames, it will be incompatible with other vendors who default VLAN 1 as untagged. Therefore, unless you are prepared to change the default behavior in MikroTik and/or other vendors, it is simpler to use VLAN 2 and higher.