diff --git a/.gitattributes b/.gitattributes
index fa5a5af1574..12b1638505d 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -2,5 +2,6 @@
 /src/test/resources/com/puppycrawl/tools/checkstyle/checks/newlineatendoffile/InputNewlineAtEndOfFileLf.java eol=lf
 /src/test/resources/com/puppycrawl/tools/checkstyle/checks/newlineatendoffile/InputNewlineAtEndOfFileCrlf.java eol=crlf
 /src/test/resources/com/puppycrawl/tools/checkstyle/checks/newlineatendoffile/InputNewlineAtEndOfFileCr.java -text
+/src/test/resources/com/puppycrawl/tools/checkstyle/checks/newlineatendoffile/InputNewlineAtEndOfFileNewlineAtEndLf.txt eol=lf
 /src/test/resources/com/puppycrawl/tools/checkstyle/grammar/InputNewlineCrAtEndOfFile.java -text
 /src/test/resources/com/puppycrawl/tools/checkstyle/grammar/javadoc/javadocTags/InputSpaceBeforeDescriptionInBlockJavadocTags.javadoc eol=lf
diff --git a/config/checkstyle_non_main_files_suppressions.xml b/config/checkstyle_non_main_files_suppressions.xml
index 29d56b4ada0..1b378906742 100644
--- a/config/checkstyle_non_main_files_suppressions.xml
+++ b/config/checkstyle_non_main_files_suppressions.xml
@@ -8,7 +8,7 @@
 
     <!-- Input files for NewlineAtEndOfFileCheckTest, intentional no new line at the end. -->
     <suppress checks="NewlineAtEndOfFile"
-              files="[\\/]test[\\/].*[\\/]InputNewlineAtEndOfFile.*\.java"/>
+              files="[\\/]test[\\/].*[\\/]InputNewlineAtEndOfFile.*\.(java|txt)"/>
 
     <!-- Intentional no new line at the end. -->
      <suppress checks="NewlineAtEndOfFile"
diff --git a/src/main/java/com/puppycrawl/tools/checkstyle/checks/LineSeparatorOption.java b/src/main/java/com/puppycrawl/tools/checkstyle/checks/LineSeparatorOption.java
index 637f1e3cfd6..61b4b93addd 100644
--- a/src/main/java/com/puppycrawl/tools/checkstyle/checks/LineSeparatorOption.java
+++ b/src/main/java/com/puppycrawl/tools/checkstyle/checks/LineSeparatorOption.java
@@ -42,7 +42,7 @@ public enum LineSeparatorOption {
      * Matches CR, LF and CRLF line separators.
      * Only the length is used - the actual value is ignored.
      */
-    LF_CR_CRLF("##"),
+    LF_CR_CRLF("#"),
 
     /** System default line separators. **/
     SYSTEM(System.getProperty("line.separator"));
@@ -69,8 +69,7 @@ public boolean matches(byte... bytes) {
         if (this == LF_CR_CRLF) {
             // this silently assumes LF and CR are of length 1
             // CRLF always matches LF, so CRLF isn't tested
-            result = LF.matches(Arrays.copyOfRange(bytes, 1, 2))
-                || CR.matches(Arrays.copyOfRange(bytes, 1, 2));
+            result = LF.matches(bytes) || CR.matches(bytes);
         }
         else {
             result = Arrays.equals(bytes, lineSeparator);
diff --git a/src/test/java/com/puppycrawl/tools/checkstyle/checks/NewlineAtEndOfFileCheckTest.java b/src/test/java/com/puppycrawl/tools/checkstyle/checks/NewlineAtEndOfFileCheckTest.java
index 4d38fca886f..1676e262fdd 100644
--- a/src/test/java/com/puppycrawl/tools/checkstyle/checks/NewlineAtEndOfFileCheckTest.java
+++ b/src/test/java/com/puppycrawl/tools/checkstyle/checks/NewlineAtEndOfFileCheckTest.java
@@ -180,6 +180,18 @@ public void testFileWithEmptyLineOnly() throws Exception {
                 expected);
     }
 
+    @Test
+    public void testFileWithEmptyLineOnlyWithLfCrCrlf() throws Exception {
+        final DefaultConfiguration checkConfig =
+                createModuleConfig(NewlineAtEndOfFileCheck.class);
+        checkConfig.addAttribute("lineSeparator", LineSeparatorOption.LF_CR_CRLF.toString());
+        final String[] expected = CommonUtil.EMPTY_STRING_ARRAY;
+        verify(
+                createChecker(checkConfig),
+                getPath("InputNewlineAtEndOfFileNewlineAtEndLf.txt"),
+                expected);
+    }
+
     @Test
     public void testWrongFile() throws Exception {
         final DefaultConfiguration checkConfig = createModuleConfig(NewlineAtEndOfFileCheck.class);
diff --git a/src/test/resources/com/puppycrawl/tools/checkstyle/checks/newlineatendoffile/InputNewlineAtEndOfFileNewlineAtEndLf.txt b/src/test/resources/com/puppycrawl/tools/checkstyle/checks/newlineatendoffile/InputNewlineAtEndOfFileNewlineAtEndLf.txt
new file mode 100644
index 00000000000..8b137891791
--- /dev/null
+++ b/src/test/resources/com/puppycrawl/tools/checkstyle/checks/newlineatendoffile/InputNewlineAtEndOfFileNewlineAtEndLf.txt
@@ -0,0 +1 @@
+