I have bought recently some newer ATMega88PA which version 5.1 of AVRDUDE didn't recognized.

Searching online for a solution I came to two ways of use the Mega88PA:

1) copy the entire mega88 section inside avrdude.conf file

2) use a newer version of AVRDUDE (avrdude-6.2-mingw32.zip)

Either solution will work, but both WINAVR and ATMEL AVR TOOLCHAIN that I have installed in my PC have put avrdude path in windows PATH environment variable. So before update AVRDUDE or edit the avrdude.conf file it is necessary to check in windows path if you are dealing with the correct files. The best is to leave only one AVRDUDE.exe (and AVRDUDE.CONF) and rename or remove any other instance of such files.

For the bootloader, just edit the makefile for atmega88 (without the P) and after compiling type the following command to upload the bootloader. If you're using USBASP insert the "low speed" jumper.

>avrdude -cusbasp -pm88p -U flash:w:main.hex:i

Then type the command below to program the fuses.

>avrdude -cusbasp -pm88p -U hfuse:w:0xd6:m -U lfuse:w:0xdf:m -U efuse:w:0xf8:m