Methods for transmitting application specific or extended commands between a host and a memory card are disclosed. Commands for an extended card protocol are embedded in messages, along with a marker, in the data or command portion of a base card transmission protocol that is used to communicate between the host and the memory card. This allows for the transmission of application specific commands that lack a corresponding command in the base card protocol. The method can be implemented on the host side at the device driver level or the file level. In order to implement a read command in the extended card protocol, a write command in the base card protocol with an encapsulated read command in the extended protocol is first sent to a logical address, followed by a read command to the same logical address. Message set identifiers associate embedded commands and data received in separate transmissions.