When attempting to SSH into an Amazon EC2 instance from a new Ubuntu machine while existing connections work fine, the Permission denied (publickey) error typically indicates one of these scenarios:

• Key pair mismatch between client and EC2 instance
• Incorrect file permissions on the local private key
• SSH agent configuration issues
• EC2 security group restrictions
• Instance user account configuration problems

Before diving deep, let's verify some basic configurations:

# Check SSH command syntax (replace values accordingly)
ssh -i ~/.ssh/your-key.pem ec2-user@ec2-xx-xxx-xxx-xxx.compute-1.amazonaws.com

# Verify key file permissions
ls -la ~/.ssh/your-key.pem
# Should show -rw------- (600) permissions

If you're certain the key pair is correct but still getting denied:

# Regenerate public key from private key if needed
ssh-keygen -y -f ~/.ssh/your-key.pem > ~/.ssh/your-key.pub

# Then update authorized_keys on EC2 instance
# (From a working connection):
echo "$(cat ~/.ssh/your-key.pub)" >> ~/.ssh/authorized_keys
chmod 600 ~/.ssh/authorized_keys

Create or modify your SSH config file for easier connections:

# ~/.ssh/config contents
Host my-ec2-instance
  HostName ec2-xx-xxx-xxx-xxx.compute-1.amazonaws.com
  User ec2-user
  IdentityFile ~/.ssh/your-key.pem
  IdentitiesOnly yes

Verify your EC2 security group allows SSH (port 22) from your current public IP:

# Get your current public IP
curl ifconfig.me

# AWS CLI command to update security group
aws ec2 authorize-security-group-ingress \
  --group-id sg-xxxxxxxx \
  --protocol tcp \
  --port 22 \
  --cidr $(curl -s ifconfig.me)/32

Add verbose flags to identify where the handshake fails:

ssh -vvv -i ~/.ssh/your-key.pem ec2-user@your-instance

Look for these critical messages in the output:

• "Offering public key" - Shows if your key is being presented
• "Server accepts key" - Indicates key authentication progress
• "Authentication succeeded" - Confirms successful login

If all else fails, consider these approaches:

# Use AWS Session Manager (requires SSM agent on instance)
aws ssm start-session --target i-xxxxxxxxxxxxx

# EC2 Instance Connect (for supported regions)
aws ec2-instance-connect send-ssh-public-key \
  --instance-id i-xxxxxxxxxxxxx \
  --availability-zone us-east-1a \
  --instance-os-user ec2-user \
  --ssh-public-key file://~/.ssh/your-key.pub

Review these often-overlooked configuration points:

• EC2 instance IAM role permissions for SSH
• Local SSH client version compatibility issues
• Multiple key pairs attached to the instance
• Instance metadata service (IMDS) configuration

---

The "Permission denied (publickey)" error typically occurs when your SSH client fails to authenticate with the EC2 instance. This can happen even if you're using the correct key pair, due to various configuration issues.

1. Incorrect Key File Permissions

On Linux systems, SSH is very strict about file permissions. Your private key file should have 600 permissions:

chmod 600 ~/.ssh/your-key.pem

2. Wrong Key Specified in SSH Command

Make sure you're explicitly specifying the correct key file:

ssh -i ~/.ssh/your-key.pem ec2-user@your-ec2-public-dns

3. EC2 Instance Security Group Configuration

Check your EC2 security group to ensure:

• Inbound SSH (port 22) is allowed from your current IP address
• No IP restrictions are blocking your connection

Checking SSH Debug Output

Add verbose flags to get more detailed error information:

ssh -vvv -i ~/.ssh/your-key.pem ec2-user@your-ec2-public-dns

EC2 Instance User Configuration

Different Linux distributions use different default users:

• Amazon Linux: ec2-user
• Ubuntu: ubuntu
• CentOS: centos

Here's a complete example of connecting to an Ubuntu EC2 instance:

# Set proper permissions
chmod 600 ~/.ssh/ubuntu-key.pem

# Connect with verbose output
ssh -vvv -i ~/.ssh/ubuntu-key.pem ubuntu@ec2-12-34-56-78.compute-1.amazonaws.com

If you're still having issues:

1. Verify the key pair is associated with the EC2 instance
2. Check the instance's system logs in the AWS console
3. Try creating a new key pair and instance if necessary