Thats line 15 on my netbeans is why I ask

I don't know much about errors but i was assuming the "15" in the "MarkovMatrix.main(MarkovMatrix.java:15)" was referring to the line number.

Hahaha that was silly of me. I change what you said however I am still receiving one error.

Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 3
at MarkovMatrix.main(MarkovMatrix.java:15)
Java Result: 1

public class MarkovMatrix {

    public static void main(String args[]) {
        double[][] matrix = new double[3][3];
        Scanner input = new Scanner(System.in);
        System.out.println("Enter a 3-by-3 matrix row by row");
        for (int i = 0; i < matrix.length; i++) {
            for (int j = 0; j < matrix[i].length; i++) {
                matrix[i][j] = input.nextDouble();
            }
        }
    }

    public static boolean isMarkovMatrix(double[][] m) {
        
            for (int j = 0; j < m.length; j++){
                double sum = 0;
                for (int i = 0; i < m.length; i++) {
                    if (m[i][j] < 0) {
                        return false;
                    }
                    sum += m[i][j];
                }
            
                if (sum != 1) {
                    return false;
                }
            
        }

        return true;
    
}
}

is it something to do with this line

for (int j = 0; j < matrix[i].length; i++) {

Okay, this is what I have now I started writing this before I read your comment. But let me know what you think about it. It is still incorrect. This is the error I receive

Exception in thread "main" java.util.InputMismatchException
at java.util.Scanner.throwFor(Scanner.java:840)
at java.util.Scanner.next(Scanner.java:1461)
at java.util.Scanner.nextInt(Scanner.java:2091)
at java.util.Scanner.nextInt(Scanner.java:2050)
at MarkovMatrix.main(MarkovMatrix.java:16)
Java Result: 1

import java.util.*;

public class MarkovMatrix {

    public static void main(String args[]) {
        int[][] matrix = new int[3][3];
        Scanner input = new Scanner(System.in);
        System.out.println("Enter a 3-by-3 matrix row by row");
        for (int i = 0; i < matrix.length; i++) {
            for (int j = 0; j < matrix[i].length; i++) {
                matrix[i][j] = input.nextInt();
            }
        }
    }

    public static boolean isMarkovMatrix(double[][] m) {
        
            for (int j = 0; j < m.length; j++){
                double sum = 0;
                for (int i = 0; i < m.length; i++) {
                    if (m[i][j] < 0) {
                        return false;
                    }
                    sum += m[i][j];
                }
            
                if (sum != 1) {
                    return false;
                }
            
        }

        return true;
    
}
}

I was trying to make it return false if the lengths of the two arrays were not equal

I changed it a little bit and I think this is a little better but it's still not quite right because it returns identical for:

51 5 22 6 1 4 24 54 6
51 22 25 6 1 4 24 54 6

but it should return identical

import java.util.Scanner ;

public class Exercise07_29 {
  public static void main(String[] args) {
    Scanner input = new Scanner(System.in);
    
    final int row = 3;
    final int column = 3;
    System.out.print("Enter list1: ");
    int[][] m1 = new int[row][column];    
    for (int i = 0; i < m1.length; i++)
      for (int j = 0; j < m1[0].length; j++)
        m1[i][j] = input.nextInt();

    System.out.print("Enter list2: ");
    int[][] m2 = new int[row][column];    
    for (int i = 0; i < m2.length; i++)
      for (int j = 0; j < m2[0].length; j++)
        m2[i][j] = input.nextInt();
    

    if (equals(m1, m2))
    	System.out.println("The two arrays are identical");
    else
    	System.out.println("The two arrays are not identical");
  }
  
  public static boolean equals(int[][] m1, int[][] m2) {
  	if (m1.length * m1[0].length != m2.length * m2[0].length)
  		return false;
  	
  	for (int i = 0; i < m1.length; i++)
  		for (int j = 0; j < m1[0].length; j++)
  			if (m1[i][j] != m2[i][j])
  				return true;
  		
    return true;
  } 
}

WOW that is so much since!. I feel like a clutz. Thank you so much.