A method for analysis of populations of micro-organisms, like bacterial populations of different taxonomic groups in an environment suspected to contain said bacteria, the method, comprising the steps of a) providing DNA obtained from said environment and providing thereto at least (i) a first primer set P1, comprising at least one primer p1, that is directed to at least one conserved location L1 specific for a first taxonomic group selected from the group consisting of phylum, class, order or family (ii) a second primer set P2, comprising at least one primer p2, that is directed to at least one conserved location L2 specific for a second taxonomic group selected from the group consisting of phylum, class, order or family (iii) a third primer set P3, comprising of at least one primer p3, that is directed to at least one conserved location L3 that is at least specific for micro-organisms belonging to the first taxonomic group. (iv) a fourth primer set P4, comprising of at least one primer p4, that is directed to at least one conserved location L4 that is at least specific for micro-organisms belonging to the second taxonomic group, and wherein the primer sets P1 and P3 are suitable for amplifying a region between said conserved regions L1 and L3 and wherein the primer sets P2 and P4 are suitable for amplifying the region between said conserved regions L2 and L4, wherein the first and the second primer set P1 and P2 are labeled, and wherein the label for primer set P1 is different from the label of primer set P2; b) performing an amplification reaction using said primer sets, thereby producing fragments having detectable differences in length, amount, and label; and c) detecting said differences in length, amount and label of the amplified products of step (b), preferably wherein the population of micro-organisms comprises bacteria and/or wherein the first and/or second taxonomic group is a phylum, and/or wherein said primer set P3 and said primer set P4 are identical. a) providing DNA obtained from said environment and providing thereto at least (i) a first primer set P1, comprising at least one primer p1, that is directed to at least one conserved location L1 specific for a first taxonomic group selected from the group consisting of phylum, class, order or family (ii) a second primer set P2, comprising at least one primer p2, that is directed to at least one conserved location L2 specific for a second taxonomic group selected from the group consisting of phylum, class, order or family (iii) a third primer set P3, comprising of at least one primer p3, that is directed to at least one conserved location L3 that is at least specific for micro-organisms belonging to the first taxonomic group. (iv) a fourth primer set P4, comprising of at least one primer p4, that is directed to at least one conserved location L4 that is at least specific for micro-organisms belonging to the second taxonomic group, and wherein the primer sets P1 and P3 are suitable for amplifying a region between said conserved regions L1 and L3 and wherein the primer sets P2 and P4 are suitable for amplifying the region between said conserved regions L2 and L4, wherein the first and the second primer set P1 and P2 are labeled, and wherein the label for primer set P1 is different from the label of primer set P2; (i) a first primer set P1, comprising at least one primer p1, that is directed to at least one conserved location L1 specific for a first taxonomic group selected from the group consisting of phylum, class, order or family (ii) a second primer set P2, comprising at least one primer p2, that is directed to at least one conserved location L2 specific for a second taxonomic group selected from the group consisting of phylum, class, order or family (iii) a third primer set P3, comprising of at least one primer p3, that is directed to at least one conserved location L3 that is at least specific for micro-organisms belonging to the first taxonomic group. (iv) a fourth primer set P4, comprising of at least one primer p4, that is directed to at least one conserved location L4 that is at least specific for micro-organisms belonging to the second taxonomic group, and wherein the primer sets P1 and P3 are suitable for amplifying a region between said conserved regions L1 and L3 and wherein the primer sets P2 and P4 are suitable for amplifying the region between said conserved regions L2 and L4, wherein the first and the second primer set P1 and P2 are labeled, and wherein the label for primer set P1 is different from the label of primer set P2; b) performing an amplification reaction using said primer sets, thereby producing fragments having detectable differences in length, amount, and label; and c) detecting said differences in length, amount and label of the amplified products of step (b), preferably wherein the population of micro-organisms comprises bacteria and/or wherein the first and/or second taxonomic group is a phylum, and/or wherein said primer set P3 and said primer set P4 are identical.