Loop custom post type by taxonomy (Category)

Before the loop starts use query_posts.
Available parameters are here.
Something like this:

global $wp_query;
query_posts( array( 
                    'post_type' => 'mycustomname', 
                    'tax_query' => array( 
                                           'relation' => 'AND', 
                                           array( 
                                                  'taxonomy' => 'mytaxonomyname', 
                                                  'field' => 'slug',
                                                  'terms' => array( 
                                                                    'myterm1slug',
                                                                    'myterm2slug' 
                                                                   ) 
                                                ) 
                                        ) 
                  ) 
);