diff --git a/aom/aomcx.h b/aom/aomcx.h
index 0d6ce7d..bbf1775 100644
--- a/aom/aomcx.h
+++ b/aom/aomcx.h
@@ -862,6 +862,12 @@
 
   /*!\brief Sets the denoisers block size */
   AV1E_SET_DENOISE_BLOCK_SIZE,
+
+  /*!\brief Sets the chroma subsampling x value */
+  AV1E_SET_CHROMA_SUBSAMPLING_X,
+
+  /*!\brief Sets the chroma subsampling y value */
+  AV1E_SET_CHROMA_SUBSAMPLING_Y,
 };
 
 /*!\brief aom 1-D scaling mode
@@ -1142,10 +1148,6 @@
 AOM_CTRL_USE_TYPE(AV1E_SET_COLOR_RANGE, int)
 #define AOM_CTRL_AV1E_SET_COLOR_RANGE
 
-/*!\brief
- *
- * TODO(rbultje) : add support of the control in ffmpeg
- */
 #define AOM_CTRL_AV1E_SET_RENDER_SIZE
 AOM_CTRL_USE_TYPE(AV1E_SET_RENDER_SIZE, int *)
 
@@ -1184,6 +1186,12 @@
 #define AOM_CTRL_AV1E_SET_DENOISE_BLOCK_SIZE
 #endif
 
+AOM_CTRL_USE_TYPE(AV1E_SET_CHROMA_SUBSAMPLING_X, unsigned int)
+#define AOM_CTRL_AV1E_SET_CHROMA_SUBSAMPLING_X
+
+AOM_CTRL_USE_TYPE(AV1E_SET_CHROMA_SUBSAMPLING_Y, unsigned int)
+#define AOM_CTRL_AV1E_SET_CHROMA_SUBSAMPLING_Y
+
 /*!\endcond */
 /*! @} - end defgroup aom_encoder */
 #ifdef __cplusplus
diff --git a/apps/aomenc.c b/apps/aomenc.c
index 7518e3a..25f012f 100644
--- a/apps/aomenc.c
+++ b/apps/aomenc.c
@@ -203,6 +203,12 @@
     bitdepth_enum);
 static const arg_def_t inbitdeptharg =
     ARG_DEF(NULL, "input-bit-depth", 1, "Bit depth of input");
+
+static const arg_def_t input_chroma_subsampling_x = ARG_DEF(
+    NULL, "input-chroma-subsampling-x", 1, "chroma subsampling x value.");
+static const arg_def_t input_chroma_subsampling_y = ARG_DEF(
+    NULL, "input-chroma-subsampling-y", 1, "chroma subsampling y value.");
+
 static const arg_def_t *main_args[] = { &help,
 #if CONFIG_FILEOPTIONS
                                         &use_cfg,
@@ -671,6 +677,8 @@
                                        &enable_ref_frame_mvs,
                                        &bitdeptharg,
                                        &inbitdeptharg,
+                                       &input_chroma_subsampling_x,
+                                       &input_chroma_subsampling_y,
                                        &sframe_dist,
                                        &sframe_mode,
                                        &save_as_annexb,
@@ -831,6 +839,8 @@
   struct aom_image *img;
   aom_codec_ctx_t decoder;
   int mismatch_seen;
+  unsigned int chroma_subsampling_x;
+  unsigned int chroma_subsampling_y;
 };
 
 static void validate_positive_rational(const char *msg,
@@ -1180,6 +1190,10 @@
       config->cfg.g_bit_depth = arg_parse_enum_or_int(&arg);
     } else if (arg_match(&arg, &inbitdeptharg, argi)) {
       config->cfg.g_input_bit_depth = arg_parse_uint(&arg);
+    } else if (arg_match(&arg, &input_chroma_subsampling_x, argi)) {
+      stream->chroma_subsampling_x = arg_parse_uint(&arg);
+    } else if (arg_match(&arg, &input_chroma_subsampling_y, argi)) {
+      stream->chroma_subsampling_y = arg_parse_uint(&arg);
 #if CONFIG_WEBM_IO
     } else if (arg_match(&arg, &stereo_mode, argi)) {
       config->stereo_fmt = arg_parse_enum_or_int(&arg);
@@ -2049,6 +2063,20 @@
                         input.fmt == AOM_IMG_FMT_I42016)) {
               stream->config.cfg.g_profile = 0;
               profile_updated = 1;
+            } else if (input.bit_depth == 12 &&
+                       input.file_type == FILE_TYPE_Y4M) {
+              // Note that here the input file values for chroma subsampling
+              // are used instead of those from the command line.
+              aom_codec_control(&stream->encoder, AV1E_SET_CHROMA_SUBSAMPLING_X,
+                                input.y4m.dst_c_dec_h >> 1);
+              aom_codec_control(&stream->encoder, AV1E_SET_CHROMA_SUBSAMPLING_Y,
+                                input.y4m.dst_c_dec_v >> 1);
+            } else if (input.bit_depth == 12 &&
+                       input.file_type == FILE_TYPE_RAW) {
+              aom_codec_control(&stream->encoder, AV1E_SET_CHROMA_SUBSAMPLING_X,
+                                stream->chroma_subsampling_x);
+              aom_codec_control(&stream->encoder, AV1E_SET_CHROMA_SUBSAMPLING_Y,
+                                stream->chroma_subsampling_y);
             }
             break;
           default: break;
diff --git a/av1/av1_cx_iface.c b/av1/av1_cx_iface.c
index 0598535..65f35bd 100644
--- a/av1/av1_cx_iface.c
+++ b/av1/av1_cx_iface.c
@@ -99,6 +99,9 @@
   float noise_level;
   int noise_block_size;
 #endif
+
+  unsigned int chroma_subsampling_x;
+  unsigned int chroma_subsampling_y;
 };
 
 static struct av1_extracfg default_extra_cfg = {
@@ -169,6 +172,8 @@
   0,   // noise_level
   32,  // noise_block_size
 #endif
+  0,  // chroma_subsampling_x
+  0,  // chroma_subsampling_y
 };
 
 struct aom_codec_alg_priv {
@@ -371,6 +376,9 @@
 #endif
   }
 
+  RANGE_CHECK_HI(extra_cfg, chroma_subsampling_x, 1);
+  RANGE_CHECK_HI(extra_cfg, chroma_subsampling_y, 1);
+
   return AOM_CODEC_OK;
 }
 
@@ -707,6 +715,9 @@
   }
 #endif  // CONFIG_REDUCED_ENCODER_BORDER
 
+  oxcf->chroma_subsampling_x = extra_cfg->chroma_subsampling_x;
+  oxcf->chroma_subsampling_y = extra_cfg->chroma_subsampling_y;
+
   return AOM_CODEC_OK;
 }
 
@@ -1685,6 +1696,20 @@
   return update_extra_cfg(ctx, &extra_cfg);
 }
 
+static aom_codec_err_t ctrl_set_chroma_subsampling_x(aom_codec_alg_priv_t *ctx,
+                                                     va_list args) {
+  struct av1_extracfg extra_cfg = ctx->extra_cfg;
+  extra_cfg.chroma_subsampling_x = CAST(AV1E_SET_CHROMA_SUBSAMPLING_X, args);
+  return update_extra_cfg(ctx, &extra_cfg);
+}
+
+static aom_codec_err_t ctrl_set_chroma_subsampling_y(aom_codec_alg_priv_t *ctx,
+                                                     va_list args) {
+  struct av1_extracfg extra_cfg = ctx->extra_cfg;
+  extra_cfg.chroma_subsampling_y = CAST(AV1E_SET_CHROMA_SUBSAMPLING_Y, args);
+  return update_extra_cfg(ctx, &extra_cfg);
+}
+
 static aom_codec_ctrl_fn_map_t encoder_ctrl_maps[] = {
   { AV1_COPY_REFERENCE, ctrl_copy_reference },
   { AOME_USE_REFERENCE, ctrl_use_reference },
@@ -1770,7 +1795,8 @@
   { AV1E_GET_ACTIVEMAP, ctrl_get_active_map },
   { AV1_GET_NEW_FRAME_IMAGE, ctrl_get_new_frame_image },
   { AV1_COPY_NEW_FRAME_IMAGE, ctrl_copy_new_frame_image },
-
+  { AV1E_SET_CHROMA_SUBSAMPLING_X, ctrl_set_chroma_subsampling_x },
+  { AV1E_SET_CHROMA_SUBSAMPLING_Y, ctrl_set_chroma_subsampling_y },
   { -1, NULL },
 };
 
diff --git a/av1/encoder/encoder.c b/av1/encoder/encoder.c
index 0c0c7e9..9b2fde2 100644
--- a/av1/encoder/encoder.c
+++ b/av1/encoder/encoder.c
@@ -1067,6 +1067,11 @@
         10;  // Default value (not signaled)
   }
 
+  if (cm->seq_params.bit_depth == AOM_BITS_12) {
+    cm->seq_params.subsampling_x = oxcf->chroma_subsampling_x;
+    cm->seq_params.subsampling_y = oxcf->chroma_subsampling_y;
+  }
+
   cm->width = oxcf->width;
   cm->height = oxcf->height;
   set_sb_size(&cm->seq_params,
diff --git a/av1/encoder/encoder.h b/av1/encoder/encoder.h
index 3ba1354..a47a4d7 100644
--- a/av1/encoder/encoder.h
+++ b/av1/encoder/encoder.h
@@ -309,6 +309,9 @@
   float noise_level;
   int noise_block_size;
 #endif
+
+  unsigned int chroma_subsampling_x;
+  unsigned int chroma_subsampling_y;
 } AV1EncoderConfig;
 
 static INLINE int is_lossless_requested(const AV1EncoderConfig *cfg) {