I live in Morocco for work and my wife lives back home in Egypt. Should I pay Zakat al-fitr for me in morocco and for her in Egypt or I pay the both in morocco or can I pay both of them in Egypt.

Praise be to Allah, the Lord of the World; and blessings and peace be upon our Prophet Muhammad and upon all his Family and Companions.
Zakah al-Fitr should be paid in the country where the person resides when it comes due. As the husband you are obliged to pay Zakah al-Fitr for yourself and your wife (or other members of your family, if any). Since you are in Morocco and she is in Egypt, you pay for yourself in Morocco and send her the money or arrange with her to pay for herself in Egypt. If her paying in Egypt is a hardship, you may pay for both of you in Morocco.
Allah knows best.