diff --git a/CHANGES.md b/CHANGES.md
index 9777a99e5..a409d4d66 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -6,7 +6,7 @@
 * ancestral: Improvements to command line arguments. [#1344][] (@jameshadfield)
      * Incompatible arguments are now checked, especially related to VCF vs FASTA inputs. 
      * `--vcf-reference` and `--root-sequence` are now mutually exclusive.
-
+* translate: Tree nodes are checked against the node-data JSON input to ensure sequences are present. [#1348][] (@jameshadfield)
 * translate: Improvements to command line arguments.  [#1348][] (@jameshadfield)
     * `--tree` and `--ancestral-sequences` are now required arguments.
     * separate VCF-only arguments into their own group
diff --git a/augur/translate.py b/augur/translate.py
index 461738b29..1fc73040f 100644
--- a/augur/translate.py
+++ b/augur/translate.py
@@ -20,6 +20,7 @@
 from .utils import read_node_data, load_features, write_json, get_json_name
 from treetime.vcf_utils import read_vcf
 from augur.errors import AugurError
+from textwrap import dedent
 
 class MissingNodeError(Exception):
     pass
@@ -339,7 +340,7 @@ def sequences_json(node_data_json, tree):
     Extract the full nuc sequence for each node in the provided node-data JSON.
     Returns a dict, keys are node names and values are a string of the genome sequence (nuc)
     """
-    node_data = read_node_data(node_data_json, tree)
+    node_data = read_node_data(node_data_json)
     if node_data is None:
         raise AugurError("could not read node data (incl sequences)")
     # extract sequences from node meta data
@@ -347,6 +348,14 @@ def sequences_json(node_data_json, tree):
     for k,v in node_data['nodes'].items():
         if 'sequence' in v:
             sequences[k] = v['sequence']
+    tree_nodes = {c.name for c in tree.find_clades()}
+    tree_nodes_missing_sequences = tree_nodes - set(sequences.keys())
+    if len(tree_nodes_missing_sequences):
+        raise AugurError(dedent(f"""\
+            {len(tree_nodes_missing_sequences)} nodes on the tree are missing nucleotide sequences in the node-data JSON.
+            These must be present under 'nodes' → <node_name> → 'sequence'.
+            This error may originate from using 'augur ancestral' with VCF input; in this case try using VCF output from that command here.
+            """))
     return sequences
 
 def register_parser(parent_subparsers):
@@ -412,7 +421,7 @@ def run(args):
         if len(features_without_variation):
             print("{} genes had no mutations and so have been be excluded.".format(len(features_without_variation)))  
     else:
-        sequences = sequences_json(args.ancestral_sequences, args.tree)
+        sequences = sequences_json(args.ancestral_sequences, tree)
         translations = {fname: translate_feature(sequences, feat) for fname, feat in features.items() if feat.type != 'source'}
 
     ## glob the annotations for later auspice export