diff --git a/src/main/java/io/github/classgraph/Scanner.java b/src/main/java/io/github/classgraph/Scanner.java
index ec60ffd22..bdc74ab75 100644
--- a/src/main/java/io/github/classgraph/Scanner.java
+++ b/src/main/java/io/github/classgraph/Scanner.java
@@ -482,6 +482,13 @@ public ClasspathElement newInstance(final ClasspathElementAndClassLoader classpa
                             return new ClasspathElementZip(classpathEntryPath, classpathEntry.classLoader,
                                     nestedJarHandler, scanSpec);
                         } else if (FileUtils.canReadAndIsDir(packageRootPath)) {
+                            if ("JrtFileSystem"
+                                    .equals(packageRootPath.getFileSystem().getClass().getSimpleName())) {
+                                // Ignore JrtFileSystem (#553) -- paths are of form:
+                                // /modules/java.base/module-info.class
+                                throw new IOException("Ignoring JrtFS filesystem path " + packageRootPath
+                                        + " (modules are scanned using the JPMS API)");
+                            }
                             // classpathEntryObj is a Path which points to a dir -- need to scan it recursively
                             return new ClasspathElementPathDir(classpathEntryPath, dirOrPathPackageRoot,
                                     classpathEntry.classLoader, nestedJarHandler, scanSpec);