1) Add the marker
2) find the backgroundcolor attribute for the css and change it.
Here it is:
JS
var myIcon = L.divIcon({
className: 'my-div-icon',
iconSize: [5, 5]
});
var marker = L.marker([50,-20], {icon: myIcon}).addTo(map);
marker.valueOf()._icon.style.backgroundColor = 'green'; //or any color