SAP JCo Standalone is the component that you can always use to connect to an SAP system from a Java application. JRFC was developed for J2EE applications in the WebAS JRFC; it differs from SAP JCo in the implementation of the lower layers, but has the same API. Finally, if you want to integrate SAP systems compliant to the Java Connector Architecture (JCA), you have to use JRA. JRA again uses internally JRFC for communicating with an SAP system.
From help.sap
Regards,
Prateek
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