You will need to build two graphs on the same basis, which will be good if you do not want to use any hint or something, because it will work only on one of the plots, try this -
$(document).ready(function(){ var maxVal = 13; var Bar1 = [5, 0, 10, 0, 12, 0]; var Bar2 = [0, 17, 0, 20, 0, 12 ]; var BaseVals=[0,0,0,0,0,0]; var baseTicks=['Americas','','Europe','','Asia',''] var EmptyTicks=['','','','','',''] plotbase = $.jqplot('chart3', [BaseVals], { seriesDefaults:{ renderer:$.jqplot.BarRenderer, rendererOptions: {barMargin: 10}, pointLabels: {show: false} }, axesDefaults: {show: false}, tickOptions: {showMark: false, angle: 90}, axes: { showLabel: false, xaxis: { renderer: $.jqplot.CategoryAxisRenderer, ticks: baseTicks, tickOptions: {markSize: 0} }, yaxis: { padMin: 0, min: 0, max: maxVal, showLabel: false, show: false } } }); plot2 = $.jqplot('chart3', [Bar1], { seriesColors: ["#67ce64", "#da9831","#67ce64", "#da9831"],\\this can be changed stackSeries: true, captureRightClick: true, seriesDefaults:{ renderer:$.jqplot.BarRenderer, rendererOptions: {barMargin: 10, highlightMouseOver: true}, pointLabels: {show: false} }, axesDefaults: {show: false}, tickOptions: {showMark: false}, axes: { showLabel: false, xaxis: { renderer: $.jqplot.CategoryAxisRenderer, ticks: EmptyTicks }, yaxis: { padMin: 0, min: 0, max: maxVal, showLabel: false, show: false } }, grid: {background: 'transparent', drawGridLines: false, gridLineColor: 'transparent', borderColor: 'transparent'} }); plot1 = $.jqplot('chart3', [Bar2], { stackSeries: true, captureRightClick: true, seriesColors: ["#effa38", "#37d1f8", "#5129b6","#5129b6"],
But note that you can only use tool-tip / Highlighter on one of the plots