diff --git a/repos/spack_repo/builtin/packages/bbmap/package.py b/repos/spack_repo/builtin/packages/bbmap/package.py
index 798e3c35274..fb99d675ae3 100644
--- a/repos/spack_repo/builtin/packages/bbmap/package.py
+++ b/repos/spack_repo/builtin/packages/bbmap/package.py
@@ -2,28 +2,62 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-from spack_repo.builtin.build_systems.generic import Package
+from spack_repo.builtin.build_systems.makefile import MakefilePackage
 from spack_repo.builtin.build_systems.sourceforge import SourceforgePackage
 
 from spack.package import *
 
 
-class Bbmap(Package, SourceforgePackage):
+class Bbmap(MakefilePackage, SourceforgePackage):
     """Short read aligner for DNA and RNA-seq data."""
 
-    homepage = "https://sourceforge.net/projects/bbmap/"
+    homepage = "https://bbmap.org/tools/bbmap"
     sourceforge_mirror_path = "bbmap/BBMap_38.63.tar.gz"
 
     license("BSD-3-Clause-LBNL")
 
+    version("39.59", sha256="a657b6f04f35125b31e431317927d3adc0a3d3655a36014aceb0e3fceb0d4cb0")
     version("39.01", sha256="98608da50130c47f3abd095b889cc87f60beeb8b96169b664bc9d849abe093e6")
     version("38.63", sha256="089064104526c8d696164aefa067f935b888bc71ef95527c72a98c17ee90a01f")
     version("37.78", sha256="f2da19f64d2bfb7db4c0392212668b425c96a27c77bd9d88d8f0aea90a193509")
     version("37.36", sha256="befe76d7d6f3d0f0cd79b8a01004a2283bdc0b5ab21b0743e9dbde7c7d79e8a9")
 
-    depends_on("c", type="build")  # generated
+    variant(
+        "usejni",
+        default=False,
+        description=(
+            "Compile the libbbtoolsjni library for accelerated versions of BBMap, Dedupe, "
+            "BBMerge, and IceCreamFinder"
+        ),
+    )
 
-    depends_on("java")
+    # Building BBMap's jni libraries requires gcc, per the BBMap docs
+    depends_on("c", type="build", when="+usejni")
+    requires("%c=gcc", when="+usejni")
+    depends_on("java@8:", type=("build", "link", "run"))
+
+    def edit(self, spec, prefix):
+        makefile = "makefile.linux"
+
+        if spec.satisfies("platform=darwin"):
+            makefile = "makefile.osx"
+
+        with working_dir(join_path(self.build_directory, "jni")):
+            rename(makefile, "Makefile")
+
+    @when("+usejni")
+    def build(self, spec, prefix):
+        with working_dir(join_path(self.build_directory, "jni")):
+            # BBMap comes with a pre-compiled x86_64 library that must first be removed
+            make("clean")
+            make()
+
+    @when("~usejni")
+    def build(self, spec, prefix):
+        with working_dir(join_path(self.build_directory, "jni")):
+            # When not building libbbtoolsjni, we should still remove the pre-compiled
+            # library for x86_64, as it may fail on other platforms.
+            make("clean")
 
     def install(self, spec, prefix):
         install_tree(".", prefix.bin)