HTML: 
<div id="container">
    <div id="div1"></div>
    <div id="div2"></div>
</div>

CSS:
#container {
    position:relative;
    width:400px;
    height:200px;
}
#container > div {
    position:absolute;
    top:0;
    left:0;
    min-width:400px;
    min-height:200px;
    width:400px;
    height:200px;
}
#div1 {
    background:red;
}
#div2 {
    background:blue;
}

jQuery:
$('#div1').hide();
setInterval(function() {
    $('#container div').toggle(500);
}, 2000)

Change on DIV to another Animation

css, jquery, animation

jQuery