ACF select box css color change

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You will need to store the field value in a variable and use the get_field() instead of the_field() function. From there you can introduce your own custom control structure to set the color you want.

Here is a snippet 

     <?php 
   //store the value in a variable first
   $option = get_field("status"); 
    if($option=="K dispozicii"){
     ?> <p style="color:green">$option</p> <?php
        }elseif ($option=="Obsazeno") {
           ?> <p style="color:red">$option</p> <?php 
        }
    ?>