We have a three year old website with a home page rank of 4. The site has over 4,000 pages, out of which only 1800 are now shown as indexed by Google.We tried to find out the reasons and after a lot of brainstorming we came up with some possibilities related with our own site as well as certain factors not in our direct control.

is everything ok with the sitemap?

build a sitemap, add it to Google Webmasters tools, build some backlinks for some inner pages and wait

You need to work on all your web page links, like do social book marking, inner page directory submission, blogs and so on. It will helps google to index all you pages as soon as possible.

Sitemap submitting would not guarantee a thorough page indexing for your sites while deep backlinks to your inner pages would be really helpful for this purpose.

Have a nice day,

Another reason can be if your site uses any Black Hat SEO. You have to make sure your site does not use any which affects why Google is not indexing your pages.

There's a lot of buzz about Google undergoing some major ranking and indexing changes - or a major "recrawl" of the web. Some webmasters have dubbed a recent change as the "Mayday" update.

I have personally seen a large dip in the number of pages Google has indexed for my site (which has millions of pages). Google maintains that the recent updates were purely algorithmic. However, I am seeing some low numbers of pages indexed from some pretty big sites. Either way, there definitely appears to be some shifting going on.

You can try any or all of the following:

1. Submit/create a sitemap to Google webmaster tools.
2. Create back links for your inner pages
3. Improve the link structure of your website- this will also improve the crawlability of your site.

try bookmarking those pages which are not indexed..

Work on your content and getting links, especially deep links.

Work on your content and getting links, especially deep links.

I agree - improving overall content and maybe updating the internal link structure of a site, could force the spiders to re-visit and index.

Sometime the poor internal linking also results in non indexing of pages on a site. Though all pages might have been indexed at some point of time, but after some time most inner pages might be left out. Besides having properly updated xml sitemap, one should work on ways to improve the internal linking of the pages. maybe an HTML sitemap linked to index page or group of pages references from various website pages, which are in search engine index. It should get you back on track

I also puzzle about it.I do some submission on my site,but it useless.

Get deeplinks for the pages that are not indexed particularly.

Google index your page in time, not all at once, wait and you will see.