diff --git a/docs/documentation/user_guide/features.rst b/docs/documentation/user_guide/features.rst
index c11578c..6333bfc 100644
--- a/docs/documentation/user_guide/features.rst
+++ b/docs/documentation/user_guide/features.rst
@@ -59,9 +59,14 @@ Motif Diversity Score (MDS)
 MDS (*Jiang et al. 2020*) is the normalized Shannon entropy of the end-motif
 k-mer distribution, summarizing end-motif diversity in a single number. The
 regional Motif Diversity Score (rMDS) computes that same entropy per genomic
-region (*Bandaru et al. 2026*).
-
-:Commands: ``mds`` (whole sample), ``regional-mds`` (per region)
+region (*Bandaru et al. 2026*). Because the underlying plug-in entropy
+estimator is biased downward in regions with few fragments, ``regional-mds``
+accepts an optional ``--miller-madow`` flag that applies a Miller-Madow bias
+correction, making rMDS values comparable across regions of differing depth.
+It is off by default, so existing output is unchanged unless requested.
+
+:Commands: ``mds`` (whole sample), ``regional-mds`` (per region, optionally
+   bias-corrected with ``--miller-madow``)
 
 Cleavage profile
 ----------------
diff --git a/docs/documentation/workflow/index.rst b/docs/documentation/workflow/index.rst
index 39944ed..5e9c989 100644
--- a/docs/documentation/workflow/index.rst
+++ b/docs/documentation/workflow/index.rst
@@ -179,7 +179,11 @@ Each command's options below carry the FinaleToolkit flag they map to. Optional
 (``--strand``: ``both``, ``forward``, or ``reverse``), ``*_mapq`` (``-q``),
 ``*_workers`` (``-t``).
 
-**mds** / **regional-mds**: ``*_sep`` (``-s``), ``*_header`` (``--header``).
+**mds**: ``mds_sep`` (``-s``), ``mds_header`` (``--header``).
+
+**regional-mds**: ``regional_mds_sep`` (``-s``), ``regional_mds_header``
+(``--header``), ``regional_mds_miller_madow`` (``--miller-madow``;
+Miller-Madow bias correction, off by default).
 
 **wps**: ``wps_site_bed`` (positional REGIONS), ``wps_reference`` (``-r``),
 ``wps_chrom_sizes`` (``--chrom-sizes``), ``wps_interval_size`` (``-i``),