Index: src/library/base/R/merge.R
===================================================================
--- src/library/base/R/merge.R	(revision 74280)
+++ src/library/base/R/merge.R	(working copy)
@@ -157,6 +157,14 @@
         }
 
         if(has.common.nms) names(y) <- nm.y
+        ## If by.x %in% names(y) then duplicate column names still arise,
+        ## apply suffixes to just y - this keeps backwards compatibility
+        ## when referring to by.x in the resulting data.frame
+        dupe.keyx <- intersect(nm.by, names(y))
+        if(length(dupe.keyx)) {
+          if(nzchar(suffixes[2L]))
+            names(y)[match(dupe.keyx, names(y), 0L)] <- paste(dupe.keyx, suffixes[2L], sep="")
+        }
         nm <- c(names(x), names(y))
         if(any(d <- duplicated(nm)))
             if(sum(d) > 1L)