diff --git a/ax_check_eigen.m4 b/ax_check_eigen.m4
index 02234d8..a7d070a 100644
--- a/ax_check_eigen.m4
+++ b/ax_check_eigen.m4
@@ -66,7 +66,7 @@ export EIGEN_CPPFLAGS
 
 AC_LANG_PUSH(C++)
 AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[
-@%:@include <Eigen/Dense>
+@%:@include <eigen3/Eigen/Dense>
 ]], [[
 ]])],[
 AC_MSG_RESULT(yes)
diff --git a/src/abundances.cpp b/src/abundances.cpp
index c95c2ca..cb8073f 100644
--- a/src/abundances.cpp
+++ b/src/abundances.cpp
@@ -50,7 +50,7 @@
 #include "negative_binomial_distribution.h"
 
 
-#include <Eigen/Dense>
+#include <eigen3/Eigen/Dense>
 //using Eigen::MatrixXd;
 
 //#ifdef  __USE_ISOC99
diff --git a/src/abundances.h b/src/abundances.h
index a3f8469..fd45821 100644
--- a/src/abundances.h
+++ b/src/abundances.h
@@ -18,7 +18,7 @@
 #include <boost/numeric/ublas/matrix.hpp>
 #include <boost/numeric/ublas/vector.hpp>
 
-#include <Eigen/Dense>
+#include <eigen3/Eigen/Dense>
 
 #include "hits.h"
 #include "scaffolds.h"
diff --git a/src/jensen_shannon.h b/src/jensen_shannon.h
index 96d6132..038a88a 100644
--- a/src/jensen_shannon.h
+++ b/src/jensen_shannon.h
@@ -14,7 +14,7 @@
 #include <boost/numeric/ublas/io.hpp>
 
 #include <vector>
-#include <Eigen/Dense>
+#include <eigen3/Eigen/Dense>
 
 namespace ublas = boost::numeric::ublas;
 
diff --git a/src/sampling.h b/src/sampling.h
index d430a34..368b9af 100644
--- a/src/sampling.h
+++ b/src/sampling.h
@@ -35,7 +35,7 @@
 #include <boost/random/variate_generator.hpp>
 #include <boost/math/constants/constants.hpp>
 
-#include <Eigen/Dense>
+#include <eigen3/Eigen/Dense>
 
 // Boost Cholesky factorizations in the spirit of lu.hpp
 // Written by Robbie Vogt, found at: