By the fifteenth century some mercantile za were organized by market rather than just commodity for example in certain towns. However, in the bigger cities such as Kyoto the za still tended to be organized by specific commodity and were usually concentrated in a special quarter of the city. This can still be seen today in certain cities in modern Japan such as the Zaimoku-za (timber merchants) quarter of Kamakura or the famous Gin-za (silver merchants) of Tokyo.
In their earlier forms, these organizations were not independent but were subordinate to a monastery, shrine, or a manor lord for which they served. But eventually these traders began to form quasi-independent za not only for their own protection but to increase their power and their profits. With this increasing power, many za began to have a monopolistic character by preventing competitors from obtaining raw materials within a certain area. A very powerful early za were the salt dealers of the Yamato province which controlled the salt wholesalers, retailers, and pedlars of the entire province. Eventually by the fifteenth century the za made powerful enemies by abusing their privileges and were forced to give way to other forms of mercantile organization such as "free" markets and guilds established by Oda Nobunaga.
Another famous za that I am sure most of you are familiar that has survived into modern Japan is the Yaku-za. This modern za has interests in many kinds of businesses and trades.
By the 18th and 19th centuries, the trade guilds and associations were transformed into more modern forms of business with the growth of the zaibatsu and keiretsu monopolies of the 20th century.
Reference:Sansom, George (1961). A History of Japan: 1334-1615.