diff --git a/pkg/obidefault/batch.go b/pkg/obidefault/batch.go
index d2cc10b..83e9d3a 100644
--- a/pkg/obidefault/batch.go
+++ b/pkg/obidefault/batch.go
@@ -1,6 +1,12 @@
 package obidefault
 
-var _BatchSize = 2000
+// _BatchSize is the minimum number of sequences per batch (floor).
+// Used as the minSeqs argument to RebatchBySize.
+var _BatchSize = 1
+
+// _BatchSizeMax is the maximum number of sequences per batch (ceiling).
+// A batch is flushed when this count is reached regardless of memory usage.
+var _BatchSizeMax = 2000
 
 // SetBatchSize sets the size of the sequence batches.
 //
@@ -25,10 +31,19 @@ func BatchSizePtr() *int {
 	return &_BatchSize
 }
 
+// BatchSizeMax returns the maximum number of sequences per batch.
+func BatchSizeMax() int {
+	return _BatchSizeMax
+}
+
+func BatchSizeMaxPtr() *int {
+	return &_BatchSizeMax
+}
+
 // _BatchMem holds the maximum cumulative memory (in bytes) per batch when
 // memory-based batching is requested. A value of 0 disables memory-based
 // batching and falls back to count-based batching.
-var _BatchMem = 0
+var _BatchMem = 128 * 1024 * 1024 // 128 MB default; set to 0 to disable
 var _BatchMemStr = ""
 
 // SetBatchMem sets the memory budget per batch in bytes.
diff --git a/pkg/obiiter/batchiterator.go b/pkg/obiiter/batchiterator.go
index 9e25d65..101717c 100644
--- a/pkg/obiiter/batchiterator.go
+++ b/pkg/obiiter/batchiterator.go
@@ -444,12 +444,17 @@ func (iterator IBioSequence) Rebatch(size int) IBioSequence {
 	return newIter
 }
 
-// RebatchBySize reorganises the stream into batches whose cumulative estimated
-// memory footprint does not exceed maxBytes. A single sequence larger than
-// maxBytes is emitted alone rather than dropped. minSeqs sets a lower bound on
-// batch size (in number of sequences) so that very large sequences still form
-// reasonably-sized work units; use 1 to disable.
-func (iterator IBioSequence) RebatchBySize(maxBytes int, minSeqs int) IBioSequence {
+// RebatchBySize reorganises the stream into batches bounded by two independent
+// upper limits: maxCount (max number of sequences) and maxBytes (max cumulative
+// estimated memory). A batch is flushed as soon as either limit would be
+// exceeded. A single sequence larger than maxBytes is always emitted alone.
+// Passing 0 for a limit disables that constraint; if both are 0 it falls back
+// to Rebatch(obidefault.BatchSizeMax()).
+func (iterator IBioSequence) RebatchBySize(maxBytes int, maxCount int) IBioSequence {
+	if maxBytes <= 0 && maxCount <= 0 {
+		return iterator.Rebatch(obidefault.BatchSizeMax())
+	}
+
 	newIter := MakeIBioSequence()
 
 	newIter.Add(1)
@@ -479,9 +484,9 @@ func (iterator IBioSequence) RebatchBySize(maxBytes int, minSeqs int) IBioSequen
 			source = seqs.Source()
 			for _, s := range seqs.Slice() {
 				sz := s.MemorySize()
-				// flush before adding if it would overflow, but only if
-				// we already meet the minimum sequence count
-				if bufBytes+sz > maxBytes && len(buffer) >= minSeqs {
+				countFull := maxCount > 0 && len(buffer) >= maxCount
+				memFull := maxBytes > 0 && bufBytes+sz > maxBytes && len(buffer) > 0
+				if countFull || memFull {
 					flush()
 				}
 				buffer = append(buffer, s)
diff --git a/pkg/obioptions/options.go b/pkg/obioptions/options.go
index 5a9878d..5ebb471 100644
--- a/pkg/obioptions/options.go
+++ b/pkg/obioptions/options.go
@@ -56,11 +56,15 @@ func RegisterGlobalOptions(options *getoptions.GetOpt) {
 
 	options.IntVar(obidefault.BatchSizePtr(), "batch-size", obidefault.BatchSize(),
 		options.GetEnv("OBIBATCHSIZE"),
-		options.Description("Number of sequence per batch for paralelle processing"))
+		options.Description("Minimum number of sequences per batch (floor, default 1)"))
+
+	options.IntVar(obidefault.BatchSizeMaxPtr(), "batch-size-max", obidefault.BatchSizeMax(),
+		options.GetEnv("OBIBATCHSIZEMAX"),
+		options.Description("Maximum number of sequences per batch (ceiling, default 2000)"))
 
 	options.StringVar(obidefault.BatchMemStrPtr(), "batch-mem", "",
 		options.GetEnv("OBIBATCHMEM"),
-		options.Description("Maximum memory per batch (e.g. 128K, 64M, 1G). Overrides --batch-size when set."))
+		options.Description("Maximum memory per batch (e.g. 128K, 64M, 1G; default: 128M). Set to 0 to disable."))
 
 	options.Bool("solexa", false,
 		options.GetEnv("OBISOLEXA"),
diff --git a/pkg/obitools/obiconvert/sequence_reader.go b/pkg/obitools/obiconvert/sequence_reader.go
index a5e27bc..cbda802 100644
--- a/pkg/obitools/obiconvert/sequence_reader.go
+++ b/pkg/obitools/obiconvert/sequence_reader.go
@@ -214,9 +214,7 @@ func CLIReadBioSequences(filenames ...string) (obiiter.IBioSequence, error) {
 
 	iterator = iterator.Speed("Reading sequences")
 
-	if obidefault.BatchMem() > 0 {
-		iterator = iterator.RebatchBySize(obidefault.BatchMem(), 1)
-	}
+	iterator = iterator.RebatchBySize(obidefault.BatchMem(), obidefault.BatchSizeMax())
 
 	return iterator, nil
 }