Before you start testing I would suggest you to change your trigger, it will not work properly in bulk handling case.

Mistakes :

1) In your trigger you are using update rel; dml statement in for loop

2) You will update all relationships for all contacts, so only last contact will be effective. You will see Id of last  contact in all relationship. You should only update relationship which are related to one contact.

Your trigger should be like this, use this

trigger MarkforDelAllinCon on Contact(before Update) {
set<ID> setContactID = new set<ID>();
    
        for(Contact Con: Trigger.new){
        if(Con.MarkforDelete__c == true){   
            setContactID.Add(Con.id);  
        }
        }
        MAP<ID , List<Relationship__c>> mapRelationship = new MAP<ID , List<Relationship__c>>(); 
        List<Relationship__c> tempList = new List<Relationship__c>();    
        for(Relationship__c relObj : [Select id,Mark_for_Delete__c,Contact_ID__c,Account_ID__c,Rev_Account_ID__c,Rev_Contact_ID__c  from Relationship__c Where  Contact_ID__c in :   setContactID and Mark_for_Delete__c !=: True])
            {
                 if(mapRelationship.containsKey(relObj.Contact_ID__c))
                  {
                        tempList = mapRelationship.get(relObj.Contact_ID__c)
                  }
                  else
                 {
                     tempList = new List<Relationship__c>();
                 }
                 tempList.add(relObj); 
                 mapRelationship.put(relObj.Contact_ID__c , relObj);
        
            }
        List<Relationship__c> Rel = new List<Relationship__c>(); 
        for(Contact Con: Trigger.new)
            {
            if(mapRelationship.containsKey(con.id))
               {
                     for(Relationship__c Res : mapRelationship.get(con.id))
                     { 
                        Res.Contact_ID__c  = Con.id;
                        Res.Rev_Contact_ID__c  = Con.id;            
                        Res.Mark_for_Delete__c = true;
                        Rel.Add(Res);
                     } 
               } 
                                      
            }
         update Rel;  
}

 Now your test class, here it is

@isTest
private class TestMarkforDelAllinCon {
    static testMethod void myTest() {
    Test.StartTest();
    Account objAcc = new Account();
    objAcc.Name = 'testAcc1';
    objAcc.AccountNumber = 'TestA00001';
    insert objAcc;
    
    Account objAccRev = new Account();
    objAccRev.Name = 'testAcc2';
    objAccRev.AccountNumber = 'TestA00001';
    insert objAccRev;
    
    List<Contact> listToUpdate =  new List<Contact>();
    Contact con = new Contact();
    con.AccountID = objAcc.id;
    con.LastName = 'TestCon1';
    con.MarkforDelete__c = True;
    insert con;
    listToUpdate.add(con);  
    
    
    Contact ConRev = new Contact();
    ConRev.AccountID = objAcc.id;
    ConRev.LastName = 'TestCon2';
    ConRev.MarkforDelete__c = True;
    insert conRev;
    update conRev;
    listToUpdate.add(conRev);

    Relationship__c  Rel = new Relationship__c();    
    for(Integer i = 0 ; i < listToUpdate.size() ; i++)
     {
       rel.Contact_ID__c = listToUpdate.get(i);
       //Fill all other required field if any
     }
    insert Rel;
     
    Update listToUpdate;         
    Test.StopTest(); 
}

 I hope it will help you.