diff --git a/python/tskit_glue/Cargo.lock b/python/tskit_glue/Cargo.lock
index ee6c06f96..a0498cbc3 100644
--- a/python/tskit_glue/Cargo.lock
+++ b/python/tskit_glue/Cargo.lock
@@ -46,9 +46,9 @@ dependencies = [
 
 [[package]]
 name = "pyo3"
-version = "0.28.3"
+version = "0.29.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "91fd8e38a3b50ed1167fb981cd6fd60147e091784c427b8f7183a7ee32c31c12"
+checksum = "cd274650b21d4bfc26a0a47587962c1edb425f69287324355cd040c3ea66071c"
 dependencies = [
  "libc",
  "once_cell",
@@ -60,18 +60,18 @@ dependencies = [
 
 [[package]]
 name = "pyo3-build-config"
-version = "0.28.3"
+version = "0.29.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e368e7ddfdeb98c9bca7f8383be1648fd84ab466bf2bc015e94008db6d35611e"
+checksum = "c5e2a7d2f0d013342f295c048ad19237add5154a55b1c5a254c0ec93d4109078"
 dependencies = [
  "target-lexicon",
 ]
 
 [[package]]
 name = "pyo3-ffi"
-version = "0.28.3"
+version = "0.29.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7f29e10af80b1f7ccaf7f69eace800a03ecd13e883acfacc1e5d0988605f651e"
+checksum = "ca85c467da1bbc8d866eea5deff9cf29ea5f7785054a17da36e65bda9c05845b"
 dependencies = [
  "libc",
  "pyo3-build-config",
@@ -79,9 +79,9 @@ dependencies = [
 
 [[package]]
 name = "pyo3-macros"
-version = "0.28.3"
+version = "0.29.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "df6e520eff47c45997d2fc7dd8214b25dd1310918bbb2642156ef66a67f29813"
+checksum = "9ac53762fd065daa3194dd09337a38bd793a188100fd1a9304c4ab312d901771"
 dependencies = [
  "proc-macro2",
  "pyo3-macros-backend",
@@ -91,13 +91,12 @@ dependencies = [
 
 [[package]]
 name = "pyo3-macros-backend"
-version = "0.28.3"
+version = "0.29.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c4cdc218d835738f81c2338f822078af45b4afdf8b2e33cbb5916f108b813acb"
+checksum = "4ca3a1557399783172dc5bf39cfca835157732532cba56b71d2292161e53b362"
 dependencies = [
  "heck",
  "proc-macro2",
- "pyo3-build-config",
  "quote",
  "syn",
 ]
diff --git a/python/tskit_glue/Cargo.toml b/python/tskit_glue/Cargo.toml
index cd5e9cafe..2a90f2a5a 100644
--- a/python/tskit_glue/Cargo.toml
+++ b/python/tskit_glue/Cargo.toml
@@ -9,6 +9,6 @@ name = "tskit_glue"
 crate-type = ["cdylib"]
 
 [dependencies]
-pyo3 = "0.28.0"
+pyo3 = "0.29.0"
 serde = {version = "1.0.203", features = ["derive"]}
 bincode = {version = "1.3.1"}
diff --git a/python/zerocopy/Cargo.lock b/python/zerocopy/Cargo.lock
index 330c59e9f..49a846d86 100644
--- a/python/zerocopy/Cargo.lock
+++ b/python/zerocopy/Cargo.lock
@@ -253,9 +253,9 @@ dependencies = [
 
 [[package]]
 name = "pyo3"
-version = "0.28.3"
+version = "0.29.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "91fd8e38a3b50ed1167fb981cd6fd60147e091784c427b8f7183a7ee32c31c12"
+checksum = "cd274650b21d4bfc26a0a47587962c1edb425f69287324355cd040c3ea66071c"
 dependencies = [
  "libc",
  "once_cell",
@@ -267,18 +267,18 @@ dependencies = [
 
 [[package]]
 name = "pyo3-build-config"
-version = "0.28.3"
+version = "0.29.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e368e7ddfdeb98c9bca7f8383be1648fd84ab466bf2bc015e94008db6d35611e"
+checksum = "c5e2a7d2f0d013342f295c048ad19237add5154a55b1c5a254c0ec93d4109078"
 dependencies = [
  "target-lexicon",
 ]
 
 [[package]]
 name = "pyo3-ffi"
-version = "0.28.3"
+version = "0.29.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7f29e10af80b1f7ccaf7f69eace800a03ecd13e883acfacc1e5d0988605f651e"
+checksum = "ca85c467da1bbc8d866eea5deff9cf29ea5f7785054a17da36e65bda9c05845b"
 dependencies = [
  "libc",
  "pyo3-build-config",
@@ -286,9 +286,9 @@ dependencies = [
 
 [[package]]
 name = "pyo3-macros"
-version = "0.28.3"
+version = "0.29.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "df6e520eff47c45997d2fc7dd8214b25dd1310918bbb2642156ef66a67f29813"
+checksum = "9ac53762fd065daa3194dd09337a38bd793a188100fd1a9304c4ab312d901771"
 dependencies = [
  "proc-macro2",
  "pyo3-macros-backend",
@@ -298,13 +298,12 @@ dependencies = [
 
 [[package]]
 name = "pyo3-macros-backend"
-version = "0.28.3"
+version = "0.29.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c4cdc218d835738f81c2338f822078af45b4afdf8b2e33cbb5916f108b813acb"
+checksum = "4ca3a1557399783172dc5bf39cfca835157732532cba56b71d2292161e53b362"
 dependencies = [
  "heck",
  "proc-macro2",
- "pyo3-build-config",
  "quote",
  "syn",
 ]
@@ -403,7 +402,7 @@ checksum = "adb6935a6f5c20170eeceb1a3835a49e12e19d792f6dd344ccc76a985ca5a6ca"
 
 [[package]]
 name = "tskit"
-version = "0.15.0-alpha.4"
+version = "0.16.3"
 dependencies = [
  "bindgen",
  "cc",
diff --git a/python/zerocopy/Cargo.toml b/python/zerocopy/Cargo.toml
index d871e4971..2b549ae98 100644
--- a/python/zerocopy/Cargo.toml
+++ b/python/zerocopy/Cargo.toml
@@ -8,5 +8,5 @@ name = "zerocopy"
 crate-type = ["cdylib"]
 
 [dependencies]
-pyo3 = {version = "0.28.0", features = ["auto-initialize"] }
+pyo3 = {version = "0.29.0", features = ["auto-initialize"] }
 tskit = {path = "../..", features = ["bindings", "unsafe_init"]}