IT systems’ integration in manufacturing companies is currently investigated in both academia and industry. While there can be found specialized systems and standards that tackle specific, e.g., production relevant problems, little has been done in the alignment of and transformation between such industrial standards. We will present the alignment of two specialized international standards, which will foster vertical system integration through detailed mapping of related concepts: (i) the Automation Markup Language (AML) standardizes the modeling of factory shop floors on top of the XML-based Computer Aided Engineering Exchange (CAEX) data format and (ii) ISA-95 is a series of standards targeting the integration of enterprise control systems, most prominent enterprise resource planning systems and manufacturing execution systems. In order to provide higher level semantics to lower level system descriptions, we have (i) aligned elements from AML and ISA-95 in order to make explicit both overlaps and complementary concepts and (ii) defined a ruleset for referencing external ISA-95 documents/elements from AML documents. Finally, we have developed a scenario that shows the potential use case for such an entwined use of AML and ISA-95.