diff --git a/hts-sys/build.rs b/hts-sys/build.rs
index dde826bb1..a391cd7a9 100644
--- a/hts-sys/build.rs
+++ b/hts-sys/build.rs
@@ -56,9 +56,15 @@ const FILES: &[&str] = &[
     "htscodecs/htscodecs/htscodecs.c",
     "htscodecs/htscodecs/pack.c",
     "htscodecs/htscodecs/rANS_static4x16pr.c",
+    "htscodecs/htscodecs/rANS_static32x16pr_avx2.c",
+    "htscodecs/htscodecs/rANS_static32x16pr_avx512.c",
+    "htscodecs/htscodecs/rANS_static32x16pr_sse4.c",
+    "htscodecs/htscodecs/rANS_static32x16pr_neon.c",
+    "htscodecs/htscodecs/rANS_static32x16pr.c",
     "htscodecs/htscodecs/rANS_static.c",
     "htscodecs/htscodecs/rle.c",
     "htscodecs/htscodecs/tokenise_name3.c",
+    "htscodecs/htscodecs/utils.c",
 ];
 
 fn main() {
@@ -180,6 +186,35 @@ fn main() {
         println!("cargo:rerun-if-changed=htslib/hfile_s3_write.c");
     }
 
+    // pass through target-feature flags to enable special instruction
+    // support in htscodecs build.
+    // TODO: add AVX512 support once Rust has it as a target feature.
+    if let Ok(targets) = env::var("CARGO_CFG_TARGET_FEATURE") {
+        if targets.contains("avx2") {
+            cfg.flag("-mavx2");
+            config_lines.push("#define HAVE_AVX2 1");
+        }
+
+        if targets.contains("sse4.1") {
+            cfg.flag("-msse4.1");
+            config_lines.push("#define HAVE_SSE4_1 1");
+        }
+
+        if targets.contains("ssse3") {
+            cfg.flag("-mssse3");
+            config_lines.push("#define HAVE_SSSE3 1");
+        }
+
+        if targets.contains("popcnt") {
+            cfg.flag("-mpopcnt");
+            config_lines.push("#define HAVE_POPCNT 1");
+        }
+
+        if targets.contains("neon") {
+            config_lines.push("#define __ARM_NEON 1");
+        }
+    }
+
     // write out config.h which controls the options htslib will use
     {
         let mut f = std::fs::File::create(out.join("htslib").join("config.h")).unwrap();
diff --git a/hts-sys/htslib b/hts-sys/htslib
index 911cb8ec8..4e61c1282 160000
--- a/hts-sys/htslib
+++ b/hts-sys/htslib
@@ -1 +1 @@
-Subproject commit 911cb8ec8fa33a293c92dcc3c3e214f49b860dbe
+Subproject commit 4e61c128238f3e7cbb3b1f4e9c0fdb4880aa9a10