How to get certificate from specific binding C#

The certificates themselves hold absolutely no information about the bindings used in IIS, so you cannot retrieve the certificates from the machine and expect them to have anything related to IIS. You would need to query that information from IIS.

To do this, you will need add a reference to the library that can be found under %windir%\system32\inetsrv\Microsoft.Web.Administration.dll (note: IIS 7 or newer must be installed). After this, you can do something like the following to get the certificate:

ServerManager manager = new ServerManager();
Site yourSite = manager.Sites["yourSiteName"];

X509Certificate2 yourCertificate = null;

foreach (Binding binding in yourSite.Bindings)
{
    if (binding.Protocol == "https" && binding.EndPoint.ToString() == "127.0.0.1" /*your binding IP*/)
    {
        var store = new X509Store(StoreName.My, StoreLocation.LocalMachine);
        store.Open(OpenFlags.ReadOnly);
        yourCertificate = store.Certificates.Find(X509FindType.FindByThumbprint, ToHex(binding.CertificateHash), true)[0];
        break;
    }
}

public static string ToHex(byte[] ba)
{
    var hex = new StringBuilder(ba.Length * 2);
    foreach (byte b in ba) 
    {
        hex.AppendFormat("{0:x2}", b);
    }

    return hex.ToString();
}

I think Camilo's answer has a small problem. As far as I can see (tested it) the code to find the certificate does not work, because System.Convert.ToBase64String(binding.CertificateHash) does not return a valid certificate thumbprint.

My version:

    /// <summary>
    /// Returns the https certificate used for a given local IIS website.
    /// </summary>
    /// <param name="sWebsite">Website url, e.g., "https://myserver.company.com"</param>
    /// <returns>certificate, null if not found</returns>
    private X509Certificate2 FindIisHttpsCert(string sWebsite)
    {
      Uri uriWebsite = new Uri(sWebsite);
      using (ServerManager sm = new ServerManager())
      {
        string sBindingPort = string.Format(":{0}:", uriWebsite.Port);
        Binding bdBestMatch = null;
        foreach (Site s in sm.Sites)
        {
          foreach (Binding bd in s.Bindings)
          {
            if (bd.BindingInformation.IndexOf(sBindingPort) >= 0)
            {
              string sBindingHostInfo = bd.BindingInformation.Substring(bd.BindingInformation.LastIndexOf(':') + 1);
              if (uriWebsite.Host.IndexOf(sBindingHostInfo, StringComparison.InvariantCultureIgnoreCase) == 0)
              {
                if ((bd.Protocol == "https") && ((bdBestMatch == null) || (bdBestMatch.BindingInformation.Length < bd.BindingInformation.Length)))
                  bdBestMatch = bd;
              }
            }
          }
        }
        if (bdBestMatch != null)
        {
          StringBuilder sbThumbPrint = new StringBuilder();
          for (int i = 0; i < bdBestMatch.CertificateHash.Length; i++)
            sbThumbPrint.AppendFormat("{0:X2}", bdBestMatch.CertificateHash[i]);

          X509Store store = new X509Store(bdBestMatch.CertificateStoreName, StoreLocation.LocalMachine);
          store.Open(OpenFlags.ReadOnly);
          X509Certificate2Collection coll = store.Certificates.Find(X509FindType.FindByThumbprint, sbThumbPrint.ToString(), true);
          if (coll.Count > 0)
            return coll[0];
        }
      }
      return null; // if no matching site was found
    }

This function also works if multiple https sites are hosted on the same server (tested) and should work if the site uses a port other than 443 (not tested). To get Binding info, %windir%\system32\inetsrv\Microsoft.Web.Administration.dll is used, as in Camilo's answer.