diff --git a/mtca/mtca.go b/mtca/mtca.go
index 52eef80fb66..a2d52617ff0 100644
--- a/mtca/mtca.go
+++ b/mtca/mtca.go
@@ -18,9 +18,9 @@ import (
 
 	"github.com/aws/aws-sdk-go-v2/service/s3"
 	"github.com/jmhodges/clock"
+	"github.com/letsencrypt/borp"
 	"golang.org/x/mod/sumdb/tlog"
 
-	"github.com/letsencrypt/borp"
 	"github.com/letsencrypt/boulder/db"
 	"github.com/letsencrypt/boulder/identifier"
 	"github.com/letsencrypt/boulder/issuance"
diff --git a/sa/db/01-boulder_sa_next.sql b/sa/db/01-boulder_sa_next.sql
index 8b50a6ce4e7..798b9d6480e 100644
--- a/sa/db/01-boulder_sa_next.sql
+++ b/sa/db/01-boulder_sa_next.sql
@@ -251,6 +251,8 @@ ALTER TABLE `revokedCertificates` ADD KEY `issuerID_shardIdx_revokedDate_idx` (`
 
 ALTER TABLE `orders`
   ADD COLUMN `mtcLogID` varchar(255) DEFAULT NULL,
-  ADD COLUMN `mtcSerialNumber` bigint(20) unsigned DEFAULT NULL;
+  ADD COLUMN `mtcSerialNumber` bigint(20) unsigned DEFAULT NULL,
+  -- A reference to the `subtreeCheckpoints` table.
+  ADD COLUMN `mtcSubtreeID` bigint(20) unsigned DEFAULT NULL;
 
 ALTER TABLE `authz2` ADD COLUMN `beganProcessing` tinyint(1) NOT NULL DEFAULT 0;
diff --git a/sa/db/01-mtcmeta_44947_4_1_0_44.sql b/sa/db/01-mtcmeta_44947_4_1_0_44.sql
index 58639a01925..8b9a96c0d9c 100644
--- a/sa/db/01-mtcmeta_44947_4_1_0_44.sql
+++ b/sa/db/01-mtcmeta_44947_4_1_0_44.sql
@@ -26,12 +26,19 @@ CREATE TABLE `checkpoints` (
     -- This is redundant with the database/keyspace name and will be used for extra checks to ensure
     -- configuration errors can't result in using the wrong database/keyspace.
     `mtcLogID` varchar(255) NOT NULL,
+    -- An ML-DSA-44 signature over a CosignedMessage with `timestamp` and `start` both zero.
+    -- TODO(#8991): Change this to store a signed note signature line instead, since that format can
+    -- carry a nonzero `timestamp`.
     `mtcaSignature` mediumblob,
+
     -- For simplicity we start out with a hardcoded assumption of one mirror signature,
     -- the planned CQRP requirement. If requirements increase we can add more fields.
     -- `mirrorID` is an ASCII-format OID relative to 1.3.6.1.4.1.
     -- Note: these two fields start empty and are filled later.
     `mirrorID` varchar(255),
+    -- An ML-DSA-44 signature over a CosignedMessage with `timestamp` and `start` both zero.
+    -- TODO(#8991): Change this to store a signed note signature line instead, since that format can
+    -- carry a nonzero `timestamp`.
     `mirrorSignature` mediumblob,
 
     -- Signed-over data: https://ietf-plants-wg.github.io/merkle-tree-certs/draft-ietf-plants-merkle-tree-certs.html#section-5.3.1
@@ -41,11 +48,57 @@ CREATE TABLE `checkpoints` (
     `treeSize` bigint(20) unsigned NOT NULL,
     `rootHash` binary(32) NOT NULL,
 
+    -- The IDs of the one or two subtrees in the `checkpointSubtrees` table implied by the delta between
+    -- this checkpoint and the previous one. These two subtrees must cover all entries between this checkpoint
+    -- and the previous one.
+    -- The first checkpoint of an issuance log will have these both NULL. Subsequent checkpoints will have `subtreeID2` NULL
+    -- if a single subtree covers the delta.
+    `subtreeID1` bigint(20) unsigned,
+    `subtreeID2` bigint(20) unsigned,
+
     `created` datetime DEFAULT current_timestamp(),
     PRIMARY KEY (`id`),
     KEY `mtcLogID_treeSize` (`mtcLogID`, `treeSize`)
 ) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_general_ci;
 
+-- Represents the pair-of-subtrees signed every checkpoint, to put into standalone certificates.
+-- The subtrees used for landmark-relative certificates are not represented explicitly
+-- in the database.
+--
+-- Note: standalone certificates are assigned to a specific checkpoint subtree at issuance.
+-- We don't look these up dynamically by serial number, so we don't have indexes on
+-- `subtreeStart` or `subtreeEnd`. Note that if we do later add an index, we'd have to pick
+-- either `subtreeStart` or `subtreeEnd`, since indexes are hierarchical. An index on
+-- (`subtreeStart`, `subtreeEnd`) isn't better than an index on (`subtreeEnd`) for answering
+-- the question "which checkpoint subtrees include N?".
+CREATE TABLE `checkpointSubtrees` (
+    `id` bigint(20) NOT NULL AUTO_INCREMENT,
+    -- ASCII-format OID relative to 1.3.6.1.4.1
+    -- https://tlswg.org/tls-trust-anchor-ids/draft-ietf-tls-trust-anchor-ids.html#name-trust-anchor-identifiers
+    -- https://ietf-plants-wg.github.io/merkle-tree-certs/draft-ietf-plants-merkle-tree-certs.html#ca-ids
+    -- This is redundant with the database/keyspace name and will be used for extra checks to ensure
+    -- configuration errors can't result in using the wrong database/keyspace.
+    `mtcLogID` varchar(255) NOT NULL,
+    -- An ML-DSA-44 signature over a CosignedMessage with zero timestamp.
+    `mtcaSignature` mediumblob NOT NULL,
+
+    -- `mirrorID` is an ASCII-format OID relative to 1.3.6.1.4.1.
+    -- Note: these two fields start empty and are filled later.
+    `mirrorID` varchar(255),
+    -- An ML-DSA-44 signature over a CosignedMessage with zero timestamp.
+    `mirrorSignature` mediumblob,
+
+    -- Signed-over data: https://ietf-plants-wg.github.io/merkle-tree-certs/draft-ietf-plants-merkle-tree-certs.html#section-5.3.1
+    -- Note that `log_origin` and `cosigner_name` in the link above are derived from `mtcaID` and `mirrorID` respectively.
+    `subtreeStart` bigint(20) unsigned NOT NULL,
+    `subtreeEnd` bigint(20) unsigned NOT NULL,
+    `subtreeHash` binary(32) NOT NULL,
+
+    `created` datetime DEFAULT current_timestamp(),
+    PRIMARY KEY (`id`)
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_general_ci;
+
+
 CREATE TABLE `landmarks` (
     `id` bigint(20) NOT NULL AUTO_INCREMENT,
     -- ASCII-format OID relative to 1.3.6.1.4.1
diff --git a/trees/treedb/treedb.go b/trees/treedb/treedb.go
index 48faeb7cf84..19f30ad74cb 100644
--- a/trees/treedb/treedb.go
+++ b/trees/treedb/treedb.go
@@ -23,6 +23,8 @@ type CheckpointModel struct {
 	MirrorSignature []byte  `db:"mirrorSignature"`
 	TreeSize        int64   `db:"treeSize"`
 	RootHash        []byte  `db:"rootHash"`
+	SubtreeID1      *int64  `db:"subtreeID1"`
+	SubtreeID2      *int64  `db:"subtreeID2"`
 }
 
 func (c *CheckpointModel) Valid() error {
@@ -54,7 +56,8 @@ func (i *Impl) LatestCheckpoint(ctx context.Context, mtcLogID string) (*Checkpoi
 	latest := new(CheckpointModel)
 	err := i.db.SelectOne(ctx, &latest,
 		`SELECT id, checkpoints.mtcLogID, mtcaSignature, mirrorID,
-		        mirrorSignature, treeSize, rootHash
+		        mirrorSignature, treeSize, rootHash,
+		        subtreeID1, subtreeID2
 		 FROM latestCheckpoint JOIN checkpoints
 		 USING(id)
 		 WHERE latestCheckpoint.mtcLogID = ? AND