Rubuta ci gaba ga wannan sakin layi - Dangantaka tsakanin kasashen biyu tun bayan juyin mulkin Sudan na 1989
sun sami hawa da sauka. Sun kai ga nadir a 1995, lokacin da wasu bangarorin gwamnatin Sudan suka shiga cikin wani makirci da kungiyar ta'addancin Masar, Gama'a Islamiyya, ta yi, don kashe shugaban kasar Masar, Husni Mubarak, yayin da yake kan hanyarsa daga filin jirgin saman Addis Ababa zuwa taron kungiyar hadin kan Afirka (a yanzu kungiyar Tarayyar Afirka) a babban birnin Habasha. A ƙarshen 1999, fushin Masar ga Sudan ya ragu, kuma Shugaba al-Bashir ya ziyarci Masar, inda shugabannin biyu suka amince da daidaita dangantakar diflomasiyya. Al-Bashir ya koma Alkahira a shekara ta 2002, a lokacin ne suka fadada hadin kai a kan batutuwa da dama. Mubarak ya biya ziyarar ta hanyar zuwa Khartoum a shekara mai zuwa. A cikin 2004 al-Bashir ya sake zuwa Alkahira, inda shugabannin biyu suka rattaba hannu kan Yarjejeniyar 'Yanci Hudu da ke magana da' yancin mallaka, motsi, zama, da aiki tsakanin kasashen biyu. An sami hadin kai kan ayyukan yaki da ta'addanci da ayyukan ci gaba da ke jan ruwa daga Kogin Nilu, kuma gwamnatocin biyu sun amince da kafa yankin cinikayya kyauta a kan iyakar Sudan-Masar, inda za su yi musayar kayayyaki ba tare da haraji ba. Sudan ta yi godiya musamman ga goyon bayan da Masar ke bayarwa a baki da kuma halin kirki ga manufofinta a Darfur. Har ila yau, Masar ta aika da dakarun soji zuwa Ofishin Jakadancin Majalisar Dinkin Duniya na Tarayyar Afirka a Darfur. Zuba jari na Masar a Sudan ya kai dalar Amurka biliyan 2.5 a shekarar 2008 yayin da zuba jari na Sudan a Masar ya kai kusan dalar Amurka miliyan 200. Zuwa shekarar 2010 dangantakar Masar da Sudan ta fi kyau fiye da yadda suka kasance a cikin shekaru da yawa, kodayake batutuwa da yawa na dogon lokaci, kamar matsayin Sudan ta Kudu na gaba, mallakar Hala<unk>ib Triangle, da kuma amfani da ruwan Nilu, ba a warware su ba.