Named as a replacement is Gustavo Hernandez Garcia, currently sub-director of planning and evaluation in Pemex's exploration and production division.
Morales Gil's resignation comes amid other massive changes rippling through the company, which is seeing its oil sector open up to private investment for the first time since 1938 with constitutional reforms passed late last year.
Morales Gil has led the exploration unit for the past nine years, capping a career of more than three decades at the state company.
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