diff --git a/autoload/ale/highlight.vim b/autoload/ale/highlight.vim
index 54103aa9..8d70ead5 100644
--- a/autoload/ale/highlight.vim
+++ b/autoload/ale/highlight.vim
@@ -34,17 +34,35 @@ function! s:GetALEMatches() abort
     return l:list
 endfunction
 
+function! s:GetCurrentMatchIDs(loclist) abort
+    let l:current_id_map = {}
+
+    for l:item in a:loclist
+        if has_key(l:item, 'match_id')
+            let l:current_id_map[l:item.match_id] = 1
+        endif
+    endfor
+
+    return l:current_id_map
+endfunction
+
 function! ale#highlight#UpdateHighlights() abort
     let l:buffer = bufnr('%')
     let l:has_new_items = has_key(s:buffer_highlights, l:buffer)
     let l:loclist = l:has_new_items ? remove(s:buffer_highlights, l:buffer) : []
+    let l:current_id_map = s:GetCurrentMatchIDs(l:loclist)
 
     if l:has_new_items || !g:ale_enabled
         for l:match in s:GetALEMatches()
-            call matchdelete(l:match['id'])
+            if !has_key(l:current_id_map, l:match.id)
+                call matchdelete(l:match.id)
+            endif
         endfor
     endif
 
+    " Remove anything with a current match_id
+    call filter(l:loclist, '!has_key(v:val, ''match_id'')')
+
     if l:has_new_items
         for l:item in l:loclist
             let l:col = l:item.col
diff --git a/test/test_highlight_placement.vader b/test/test_highlight_placement.vader
index 2bf37d19..52e861d9 100644
--- a/test/test_highlight_placement.vader
+++ b/test/test_highlight_placement.vader
@@ -33,11 +33,13 @@ After:
   delfunction GenerateResults
   call ale#linter#Reset()
   let g:ale_buffer_info = {}
+  call clearmatches()
 
 Given testft(A Javscript file with warnings/errors):
   foo
   bar
   baz wat
+  line four
 
 Execute(Highlights should be set when a linter runs):
   call ale#Lint()
@@ -52,3 +54,23 @@ Execute(Highlights should be set when a linter runs):
   \ getmatches()
 
   AssertEqual [4, 5, 6], map(copy(g:ale_buffer_info[bufnr('')].loclist), 'v:val.match_id')
+
+Execute(Existing highlights should be kept):
+  call matchaddpos('ALEError', [[1, 2, 1]], 10, 347)
+  call matchaddpos('ALEWarning', [[2, 2, 1]], 10, 348)
+
+  call ale#highlight#SetHighlights(bufnr('%'), [
+  \ {'bufnr': bufnr('%'), 'match_id': 347, 'type': 'E', 'lnum': 1, 'col': 2},
+  \ {'bufnr': bufnr('%'), 'match_id': 348, 'type': 'W', 'lnum': 2, 'col': 2},
+  \ {'bufnr': bufnr('%'), 'type': 'E', 'lnum': 3, 'col': 2},
+  \ {'bufnr': bufnr('%'), 'type': 'W', 'lnum': 4, 'col': 1},
+  \])
+
+  AssertEqual
+  \ [
+  \   {'group': 'ALEError', 'id': 347, 'priority': 10, 'pos1': [1, 2, 1]},
+  \   {'group': 'ALEWarning', 'id': 348, 'priority': 10, 'pos1': [2, 2, 1]},
+  \   {'group': 'ALEError', 'id': 7, 'priority': 10, 'pos1': [3, 2, 1]},
+  \   {'group': 'ALEWarning', 'id': 8, 'priority': 10, 'pos1': [4, 1, 1]},
+  \ ],
+  \ getmatches()